| Previous changeset 20:e21be0412789 (2015-11-19) Next changeset 22:729aac64ce43 (2015-11-19) |
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Commit message:
Uploaded |
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modified:
pre_process_protein_name_set.R |
| b |
| diff -r e21be0412789 -r 9e0a894d2676 pre_process_protein_name_set.R --- a/pre_process_protein_name_set.R Thu Nov 19 13:31:59 2015 -0500 +++ b/pre_process_protein_name_set.R Thu Nov 19 13:38:20 2015 -0500 |
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| @@ -26,7 +26,7 @@ library(VennDiagram) ##### #data -main <- function(peptides_file) { +main <- function(peptides_file, db_path) { peptides_file = read.delim(peptides_file,header=TRUE,stringsAsFactors=FALSE,fill=TRUE) peptides_txt = peptides_file intensity_columns = names(peptides_txt[,str_detect(names(peptides_txt),"Intensity\\.*")]) #Pulls out all lines with Intensity in them. @@ -36,7 +36,7 @@ peptides_txt_mapped = subset(peptides_txt_mapped,!is.na(Uniprot)) #removes reverse sequences and any that didn't match a uniprot accession columns_comb = c("Uniprot", intensity_columns) peptides_mapped_intensity = subset(peptides_txt_mapped, select = columns_comb) #Subsets out only the needed cloumns for Tukeys (Uniprot IDS and baited intensities) - swissprot_fasta = scan("/home/philip/galaxy/tools/Moffitt_Tools/uniprot_names.txt",what="character") + swissprot_fasta = scan(db_path, what="character") peptides_txt_mapped_log2 = peptides_mapped_intensity # Takes the log2 of the intensities. for (i in intensity_columns) { @@ -95,4 +95,4 @@ } args <- commandArgs(trailingOnly = TRUE) -main(args[1]) +main(args[1], args[2]) |