Mercurial > repos > bornea > saint_preprocessing

comparison pre_process_protein_name_set.R @ 30:e6e456d3ac14 draft

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author bornea
date Tue, 26 Apr 2016 16:16:56 -0400
parents dbd1af88f060
children 63008bdf576e
comparison
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29:bd71998aec8d 30:e6e456d3ac14
86 print("Uniprot Database does not have any of the proteins in the peptides file") 86 print("Uniprot Database does not have any of the proteins in the peptides file")
87 quit() 87 quit()
88 } 88 }
89 protein_intensities_tukeys = get_protein_values(peptides_txt_mapped_log2,intensity_columns) 89 protein_intensities_tukeys = get_protein_values(peptides_txt_mapped_log2,intensity_columns)
90 protein_intensities_tukeys[protein_intensities_tukeys == 1] <- 0 90 protein_intensities_tukeys[protein_intensities_tukeys == 1] <- 0
91 write.table(protein_intensities_tukeys, "./tukeys_output.txt", row.names = FALSE, col.names = TRUE, quote = FALSE, sep = "\t") 91 # Eliminates all pure NA rows.
92 protein_intensities_tukeys = protein_intensities_tukeys[rowSums(is.na(protein_intensities_tukeys)) != (ncol(protein_intensities_tukeys)-1),]
93 write.table(protein_intensities_tukeys, "./tukeys_output.txt", row.names = FALSE, col.names = TRUE, quote = FALSE, sep = "\t")
92 94
93 } 95 }
94 96
95 map_peptides_proteins = function(peptides_in) { 97 map_peptides_proteins = function(peptides_in) {
96 peptides_in = subset(peptides_in,peptides_in$Proteins != "") 98 peptides_in = subset(peptides_in,peptides_in$Proteins != "")