spreadPepNums: Spreads peptide numbers.

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

Spreads peptide numbers.

Description

Spreads fields of numeric values: sd_log2_R, log2_R, log2_R, I, N_I by TMT sets.

Usage

spreadPepNums(
  df,
  dat_dir = NULL,
  basenames,
  tmt_plex = 0L,
  ok_lfq = FALSE,
  group_psm_by = "pep_seq_mod",
  group_pep_by = "gene",
  engine = "mz"
)

Arguments

df	A data frame of peptide table, ordered by ascending TMT_Set and LCMS_Injection.
dat_dir	The working directory.
basenames	Names of peptide table files.
tmt_plex	The multiplicity of TMT; zero for LFQ.
ok_lfq	Logical Capable of LFQ or not.
group_psm_by	Group PSMs by.
group_pep_by	Groups peptides by.
engine	The search engine.

Details

Also works for LFQ as each sample corresponds to a TMT set.

For single SILAC sample, the values of log2Ratios spreads into MULTIPLE columns of heavy, light etc. Despite, log2Ratios remains NA, just like regular single-sample LFQ. The log2Ratios will be later calculated with calcLFQPepNums that are based on intensity values.

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