calculateFDR: Perform global or separate FDR estimation

In wenbostar/PGA: An package for identification of novel peptides by customized database derived from RNA-Seq

Perform global or separate FDR estimation

Description

Perform global or separate FDR estimation

Usage

calculateFDR(psmfile = NULL, db = NULL, fdr = 0.01,
  peptide_level = FALSE, decoyPrefix = "###REV###",
  novelPrefix = NULL, better_score_lower = TRUE, remap = FALSE,
  out_dir = "./", protein_inference = FALSE, score_t = 1, xmx = 2,
  verbose = 1)

Arguments

psmfile	PSM file in TSV format
db	A FASTA format database file used for MS/MS searching.
fdr	FDR cutoff, default is 0.01
peptide_level	Peptide level FDR, default is FALSE
decoyPrefix	The prefix of decoy sequences ID. Default is "###REV###". "###REV###" is the prefix which used by function dbCreator.
novelPrefix	The prefix of novel protein ID. Default is NULL. If the value is NULL, it will perform global FDR estimation. Otherwise, it will perform separate FDR estimation for novel peptides.
better_score_lower	TRUE: lower score is better, FALSE: higher score is better. Default is TRUE.
remap	TRUE: re-map peptide to protein, FALSE: use the peptide protein mapping data in the PSM file. Default is FALSE.
out_dir	Output directory.
protein_inference	Whether or not to perform protein inference. Default is FALSE
score_t	Score transformation for score distribution plot. 0: no transformation, 1: -log(score).
xmx	The maximum Java heap size. The unit is "G". Default is 2.
verbose	Output level. Default is 1.

Value

none

wenbostar/PGA documentation built on March 24, 2022, 6:48 p.m.