Mercurial > repos > proteore > proteore_clusterprofiler

annotate GO-enrich.R @ 4:18275725e7cf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
author proteore
date Mon, 17 Sep 2018 10:30:30 -0400
parents 67a796154e2a
children 36c586c918eb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
1 suppressMessages(library(clusterProfiler,quietly = TRUE))
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
2
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
3 # Read file and return file content as data.frame
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
4 readfile = function(filename, header) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
5 if (header == "true") {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
6 # Read only first line of the file as header:
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
7 headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
8 #Read the data of the files (skipping the first row)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
9 file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
10 # Remove empty rows
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
11 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
12 #And assign the header to the data
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
13 names(file) <- headers
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
14 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
15 else {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
16 file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "")
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
17 # Remove empty rows
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
18 file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
19 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
20 return(file)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
21 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
22
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
23 max_str_length_10_first <- function(vector){
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
24 vector <- as.vector(vector)
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
25 nb_description = length(vector)
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
26 if (nb_description >= 10){nb_description=10}
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
27 return(max(nchar(vector[1:nb_description])))
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
28 }
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
29
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
30
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
31 repartition.GO <- function(geneid, orgdb, ontology, level=3, readable=TRUE) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
32 ggo<-groupGO(gene=geneid,
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
33 OrgDb = orgdb,
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
34 ont=ontology,
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
35 level=level,
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
36 readable=TRUE)
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
37
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
38 if (max_str_length_10_first(ggo$Description) > 50 ){
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
39 width=720
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
40 } else {
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
41 width=600
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
42 }
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
43
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
44 name <- paste("GGO_", ontology, "_bar-plot", sep = "")
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
45 png(name,height = 720, width = width)
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
46 p <- barplot(ggo, showCategory=10)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
47 print(p)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
48 dev.off()
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
49 return(ggo)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
50 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
51
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
52 # GO over-representation test
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
53 enrich.GO <- function(geneid, universe, orgdb, ontology, pval_cutoff, qval_cutoff,plot) {
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
54 ego<-enrichGO(gene=geneid,
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
55 universe=universe,
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
56 OrgDb=orgdb,
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
57 ont=ontology,
3
67a796154e2a planemo upload commit 07fb0efd8a1badeb395fa1dc435037998b4de25f
proteore
parents: 2
diff changeset
58 keytype="ENTREZID",
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
59 pAdjustMethod="BH",
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
60 pvalueCutoff=pval_cutoff,
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
61 qvalueCutoff=qval_cutoff,
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
62 readable=TRUE)
2
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
63
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
64 if (max_str_length_10_first(ego$Description) > 50 ){
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
65 width=800
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
66 } else {
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
67 width=600
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
68 }
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
69
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
70 # Plot bar & dot plots
2
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
71 #if there are enriched GopTerms
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
72 if (length(ego$ID)>0){
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
73 if ("dotplot" %in% plot ){
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
74 dot_name <- paste("EGO_", ontology, "_dot-plot", sep = "")
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
75 png(dot_name,height = 720, width = width)
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
76 p <- dotplot(ego, showCategory=10)
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
77 print(p)
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
78 dev.off()
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
79 }
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
80
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
81 if ("barplot" %in% plot ){
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
82 bar_name <- paste("EGO_", ontology, "_bar-plot", sep = "")
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
83 png(bar_name,height = 720, width = width)
2
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
84 p <- barplot(ego)
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
85 print(p)
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
86 dev.off()
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
87 return(ego)
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
88 }
2
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
89 } else {
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
90 warning(paste("No Go terms enriched (EGO) found for ",ontology,"ontology"),immediate. = TRUE,noBreaks. = TRUE,call. = FALSE)
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
91 }
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
92 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
93
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
94 check_ids <- function(vector,type) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
95 uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
96 entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
97 if (type == "entrez")
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
98 return(grepl(entrez_id,vector))
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
99 else if (type == "uniprot") {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
100 return(grepl(uniprot_pattern,vector))
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
101 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
102 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
103
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
104 clusterProfiler = function() {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
105 args <- commandArgs(TRUE)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
106 if(length(args)<1) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
107 args <- c("--help")
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
108 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
109
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
110 # Help section
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
111 if("--help" %in% args) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
112 cat("clusterProfiler Enrichment Analysis
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
113 Arguments:
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
114 --input_type: type of input (list of id or filename)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
115 --input: input
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
116 --ncol: the column number which contains list of input IDs
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
117 --header: true/false if your file contains a header
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
118 --id_type: the type of input IDs (UniProt/EntrezID)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
119 --universe_type: list or filename
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
120 --universe: background IDs list
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
121 --uncol: the column number which contains background IDs list
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
122 --uheader: true/false if the background IDs file contains header
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
123 --universe_id_type: the type of universe IDs (UniProt/EntrezID)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
124 --species
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
125 --onto_opt: ontology options
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
126 --go_function: groupGO/enrichGO
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
127 --level: 1-3
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
128 --pval_cutoff
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
129 --qval_cutoff
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
130 --text_output: text output filename
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
131 --plot : type of visualization, dotplot or/and barplot \n")
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
132 q(save="no")
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
133 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
134 # Parse arguments
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
135 parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
136 argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
137 args <- as.list(as.character(argsDF$V2))
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
138 names(args) <- argsDF$V1
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
139 plot = unlist(strsplit(args$plot,","))
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
140 #print(args)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
141
2
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
142 #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
1
91b9b48d07b3 planemo upload commit 4244759c3ec402d4309369b46aec75dc49e4c0b1-dirty
proteore
parents: 0
diff changeset
143 #load("/home/dchristiany/proteore_project/ProteoRE/tools/cluster_profiler/args.Rda")
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
144
2
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
145 suppressMessages(library(args$species, character.only = TRUE, quietly = TRUE))
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
146
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
147 # Extract OrgDb
2
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
148 if (args$species=="org.Hs.eg.db") {
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
149 orgdb<-org.Hs.eg.db
2
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
150 } else if (args$species=="org.Mm.eg.db") {
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
151 orgdb<-org.Mm.eg.db
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
152 } else if (args$species=="org.Rn.eg.db") {
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
153 orgdb<-org.Rn.eg.db
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
154 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
155
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
156 # Extract input IDs
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
157 input_type = args$input_type
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
158 if (input_type == "text") {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
159 input = strsplit(args$input, "[ \t\n]+")[[1]]
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
160 } else if (input_type == "file") {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
161 filename = args$input
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
162 ncol = args$ncol
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
163 # Check ncol
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
164 if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
165 stop("Please enter the right format for column number: c[number]")
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
166 } else {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
167 ncol = as.numeric(gsub("c", "", ncol))
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
168 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
169 header = args$header
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
170 # Get file content
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
171 file = readfile(filename, header)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
172 # Extract Protein IDs list
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
173 input = sapply(as.character(file[,ncol]),function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
174 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
175 id_type = args$id_type
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
176 ## Get input gene list from input IDs
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
177 #ID format Conversion
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
178 #This case : from UNIPROT (protein id) to ENTREZ (gene id)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
179 #bitr = conversion function from clusterProfiler
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
180 if (id_type=="Uniprot" & any(check_ids(input,"uniprot"))) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
181 any(check_ids(input,"uniprot"))
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
182 idFrom<-"UNIPROT"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
183 idTo<-"ENTREZID"
2
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
184 suppressMessages(gene<-bitr(input, fromType=idFrom, toType=idTo, OrgDb=orgdb))
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
185 gene<-unique(gene$ENTREZID)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
186 } else if (id_type=="Entrez" & any(check_ids(input,"entrez"))) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
187 gene<-unique(input)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
188 } else {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
189 print(paste(id_type,"not found in your ids list, please check your IDs in input or the selected column of your input file"))
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
190 stop()
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
191 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
192
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
193 ontology <- strsplit(args$onto_opt, ",")[[1]]
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
194 ## Extract GGO/EGO arguments
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
195 if (args$go_represent == "true") {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
196 go_represent <- args$go_represent
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
197 level <- as.numeric(args$level)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
198 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
199 if (args$go_enrich == "true") {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
200 go_enrich <- args$go_enrich
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
201 pval_cutoff <- as.numeric(args$pval_cutoff)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
202 qval_cutoff <- as.numeric(args$qval_cutoff)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
203 # Extract universe background genes (same as input file)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
204 if (!is.null(args$universe_type)) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
205 universe_type = args$universe_type
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
206 if (universe_type == "text") {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
207 universe = strsplit(args$universe, "[ \t\n]+")[[1]]
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
208 } else if (universe_type == "file") {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
209 universe_filename = args$universe
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
210 universe_ncol = args$uncol
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
211 # Check ncol
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
212 if (! as.numeric(gsub("c", "", universe_ncol)) %% 1 == 0) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
213 stop("Please enter the right format for column number: c[number]")
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
214 } else {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
215 universe_ncol = as.numeric(gsub("c", "", universe_ncol))
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
216 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
217 universe_header = args$uheader
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
218 # Get file content
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
219 universe_file = readfile(universe_filename, universe_header)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
220 # Extract Protein IDs list
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
221 universe <- sapply(universe_file[,universe_ncol], function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
222 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
223 universe_id_type = args$universe_id_type
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
224 ##to initialize
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
225 if (universe_id_type=="Uniprot" & any(check_ids(universe,"uniprot"))) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
226 idFrom<-"UNIPROT"
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
227 idTo<-"ENTREZID"
2
1c98865a8508 planemo upload commit 01102a33a5c3fc56de61cd12784691b49334054b-dirty
proteore
parents: 1
diff changeset
228 suppressMessages(universe_gene<-bitr(universe, fromType=idFrom, toType=idTo, OrgDb=orgdb))
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
229 universe_gene<-unique(universe_gene$ENTREZID)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
230 } else if (universe_id_type=="Entrez" & any(check_ids(universe,"entrez"))) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
231 universe_gene<-unique(universe)
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
232 } else {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
233 if (universe_type=="text"){
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
234 print(paste(universe_id_type,"not found in your background IDs list",sep=" "))
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
235 } else {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
236 print(paste(universe_id_type,"not found in the column",universe_ncol,"of your background IDs file",sep=" "))
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
237 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
238 universe_gene = NULL
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
239 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
240 } else {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
241 universe_gene = NULL
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
242 }
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
243 } else {
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
244 universe_gene = NULL
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
245 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
246
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
247 ##enrichGO : GO over-representation test
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
248 for (onto in ontology) {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
249 if (args$go_represent == "true") {
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
250 ggo<-repartition.GO(gene, orgdb, onto, level, readable=TRUE)
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
251 output_path = paste("cluster_profiler_GGO_",onto,".csv",sep="")
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
252 write.table(ggo, output_path, sep="\t", row.names = FALSE, quote=FALSE)
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
253 }
4
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
254
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
255 if (args$go_enrich == "true") {
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
256 ego<-enrich.GO(gene, universe_gene, orgdb, onto, pval_cutoff, qval_cutoff,plot)
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
257 output_path = paste("cluster_profiler_EGO_",onto,".csv",sep="")
18275725e7cf planemo upload commit 9bdfcce89bdea8a0a85bfbf8f0fa9b943b17bea1-dirty
proteore
parents: 3
diff changeset
258 write.table(ego, output_path, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE)
0
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
259 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
260 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
261 }
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
262
076349b72690 planemo upload commit 2e441b4969ae7cf9aeb227a1d47c43ef7268a5e6-dirty
proteore
parents:
diff changeset
263 clusterProfiler()