Mercurial > repos > eschen42 > mqppep_preproc

comparison MaxQuantProcessingScript.R @ 6:42daf70d4ed4 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
author eschen42
date Fri, 11 Mar 2022 20:04:40 +0000
parents b91809a18dbe
children 36f183e5e4ed
comparison
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5:b91809a18dbe 6:42daf70d4ed4
519 519
520 # Write quantitative values for debugging purposes 520 # Write quantitative values for debugging purposes
521 # --- 521 # ---
522 quant_write <- cbind(metadata_df[, "Sequence window"], quant_data) 522 quant_write <- cbind(metadata_df[, "Sequence window"], quant_data)
523 colnames(quant_write)[1] <- "Sequence.Window" 523 colnames(quant_write)[1] <- "Sequence.Window"
524 write.table(
525 quant_write,
526 file = quant_file_name,
527 sep = "\t",
528 quote = FALSE,
529 col.names = TRUE,
530 row.names = FALSE
531 )
524 # ... 532 # ...
525 533
526 534
527 # Make new data frame containing only Phosphopeptides 535 # Make new data frame containing only Phosphopeptides
528 # that are to be mapped to quant data (merge_df) 536 # that are to be mapped to quant data (merge_df)
566 nrow(quant_data_qc) - nrow(quant_data_qc_collapsed) 574 nrow(quant_data_qc) - nrow(quant_data_qc_collapsed)
567 ) / (2 * nrow(quant_data_qc)) 575 ) / (2 * nrow(quant_data_qc))
568 pct_multiphos <- sprintf("%0.1f%s", 100 * pct_multiphos, "%") 576 pct_multiphos <- sprintf("%0.1f%s", 100 * pct_multiphos, "%")
569 # ... 577 # ...
570 578
571 write.table(
572 quant_data_qc_collapsed,
573 file = quant_file_name,
574 sep = "\t",
575 quote = FALSE,
576 col.names = TRUE,
577 row.names = FALSE
578 )
579 579
580 # Compute and visualize breakdown of pY, pS, and pT before enrichment filter 580 # Compute and visualize breakdown of pY, pS, and pT before enrichment filter
581 # --- 581 # ---
582 py_data <- 582 py_data <-
583 quant_data_qc_collapsed[ 583 quant_data_qc_collapsed[