add_shared_sm_genes: Find peptides that are shared by genes.

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Find peptides that are shared by genes.

Description

For Spectrum Mill with duplicates, such as P06748|Q61937|P06748|Q61937, removals under accession_numbers.

Usage

add_shared_sm_genes(
  df = NULL,
  key = "Proteins",
  sep = ";",
  fasta = NULL,
  entrez = NULL
)

Arguments

df	PSM data.
key	the column key of mapped proteins.
sep	Character string; the separator of the mapped proteins.
fasta	Character string(s) to the name(s) of fasta file(s) with prepended directory path. The fasta database(s) need to match those used in MS/MS ion search. There is no default and users need to provide the correct file path(s) and name(s).
entrez	Character string(s) to the name(s) of entrez file(s) with prepended directory path. At the NULL default, a convenience lookup is available for species among c("human", "mouse", "rat"). For other species, users need to provide the file path(s) and name(s) for the lookup table(s). See also Uni2Entrez and Ref2Entrez for preparing custom entrez files.

qzhang503/proteoQ documentation built on Feb. 27, 2025, 8:34 a.m.