Mercurial > repos > greg > multilocus_genotype

comparison multilocus_genotype.R @ 2:86aaadf36a4f draft

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author greg
date Thu, 25 Oct 2018 11:10:17 -0400
parents 725b160c91f0
children 1bc815d9c8c5
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1:ba2df0561b12 2:86aaadf36a4f
7 suppressPackageStartupMessages(library("ape")) 7 suppressPackageStartupMessages(library("ape"))
8 suppressPackageStartupMessages(library("ggplot2")) 8 suppressPackageStartupMessages(library("ggplot2"))
9 suppressPackageStartupMessages(library("knitr")) 9 suppressPackageStartupMessages(library("knitr"))
10 10
11 option_list <- list( 11 option_list <- list(
12 make_option(c("--input_vcf"), action="store", dest="input_vcf", help="VCF input file") 12 make_option(c("--input_vcf"), action="store", dest="input_vcf", help="VCF input file"),
13 make_option(c("--input_pop_info"), action="store", dest="input_pop_info", help="Population information input file") 13 make_option(c("--input_pop_info"), action="store", dest="input_pop_info", help="Population information input file")
14 ) 14 )
15 15
16 parser <- OptionParser(usage="%prog [options] file", option_list=option_list); 16 parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
17 args <- parse_args(parser, positional_arguments=TRUE); 17 args <- parse_args(parser, positional_arguments=TRUE);
26 provesti_distance <- function(distance, selection) { 26 provesti_distance <- function(distance, selection) {
27 eval(parse(text=paste("as.matrix(distance)[", selection, "]"))); 27 eval(parse(text=paste("as.matrix(distance)[", selection, "]")));
28 } 28 }
29 29
30 #Read in VCF input file. 30 #Read in VCF input file.
31 vcf <- read.vcfR(opts$input_vcf); 31 vcf <- read.vcfR(opt$input_vcf);
32 32
33 # Convert VCF file into formats compatiable with the Poppr package. 33 # Convert VCF file into formats compatiable with the Poppr package.
34 gind <- vcfR2genind(vcf); 34 gind <- vcfR2genind(vcf);
35 # Add population information to the genind object. 35 # Add population information to the genind object.
36 poptab <- read.table(opt$input_pop_info, check.names=FALSE, header=T, na.strings = c("", "NA")); 36 poptab <- read.table(opt$input_pop_info, check.names=FALSE, header=T, na.strings = c("", "NA"));