comparison pre_process_protein_name_set.R @ 32:63008bdf576e draft

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31:761e1ad2b130

	peptides_txt_mapped_log2[peptides_txt_mapped_log2 == -Inf] <- NA
  #uniprot accessions WITHOUT isoforms; it looks like only contaminants contain isoforms anyways.
	mapped_protein_uniprotonly = str_extract(peptides_txt_mapped_log2$Uniprot,"[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}") 
	mapped_protein_uniprot_accession = str_extract(peptides_txt_mapped_log2$Uniprot,"[OPQ][0-9][A-Z0-9]{3}[0-9](-[0-9]+)?|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}(-[0-9]+)?|[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}")
	peptides_txt_mapped_log2$mapped_protein = mapped_protein_uniprotonly
  # Runs the Tukey function returning completed table.
  peptides_txt_mapped_log2 = subset(peptides_txt_mapped_log2,mapped_protein %in% swissprot_fasta)
  if (nrow(peptides_txt_mapped_log2) == 0) {
    print("Uniprot Database does not have any of the proteins in the peptides file")
    quit()
  }
	protein_intensities_tukeys = get_protein_values(peptides_txt_mapped_log2,intensity_columns)

32:63008bdf576e

	peptides_txt_mapped_log2[peptides_txt_mapped_log2 == -Inf] <- NA
  #uniprot accessions WITHOUT isoforms; it looks like only contaminants contain isoforms anyways.
	mapped_protein_uniprotonly = str_extract(peptides_txt_mapped_log2$Uniprot,"[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}") 
	mapped_protein_uniprot_accession = str_extract(peptides_txt_mapped_log2$Uniprot,"[OPQ][0-9][A-Z0-9]{3}[0-9](-[0-9]+)?|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}(-[0-9]+)?|[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}")
	peptides_txt_mapped_log2$mapped_protein = mapped_protein_uniprotonly
	names_db = str_extract(swissprot_fasta,"[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}")
	names_db = names_db[!is.na(names_db)]
  # Runs the Tukey function returning completed table.
  peptides_txt_mapped_log2 = subset(peptides_txt_mapped_log2,mapped_protein %in% names_db)
  if (nrow(peptides_txt_mapped_log2) == 0) {
    print("Uniprot Database does not have any of the proteins in the peptides file")
    quit()
  }
	protein_intensities_tukeys = get_protein_values(peptides_txt_mapped_log2,intensity_columns)