countSpecs: Spectrum counts at peptide levels

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

Spectrum counts at peptide levels

Description

Spectrum counts at peptide levels

Usage

countSpecs(
  dat_dir = NULL,
  label_scheme_full = NULL,
  type = "PSM",
  filelist = NULL,
  basenames = NULL,
  set_idxes = 1L,
  injn_idxes = 1L,
  group_psm_by = "pep_seq_mod",
  group_pep_by = "prot_acc",
  pep_col = "pep_n_specs",
  prot_col = "prot_n_specs"
)

Arguments

dat_dir	The working directory.
label_scheme_full	The full label scheme.
type	The data type.
filelist	A list of file names of TMTset1_LCMSinj1_Peptide_N.txt etc with prepending path.
basenames	The base names of file names in filelist.
set_idxes	The indexes of TMT_Set's corresponding to basenames.
injn_idxes	The indexes of LCMS_Inj's corresponding to basenames.
group_psm_by	A character string specifying the method in PSM grouping. At the pep_seq default, descriptive statistics will be calculated based on the same pep_seq groups. At the pep_seq_mod alternative, peptides with different variable modifications will be treated as different species and descriptive statistics will be calculated based on the same pep_seq_mod groups.
group_pep_by	A character string specifying the method in peptide grouping. At the prot_acc default, descriptive statistics will be calculated based on the same prot_acc groups. At the gene alternative, proteins with the same gene name but different accession numbers will be treated as one group.
pep_col	The output column name for peptide summary statistics.
prot_col	The output column name for protein summary statistics.

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