annotPSM: Annotates PSM results

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

Annotates PSM results

Description

annotPSM adds fields of annotation to Mascot PSM tables after rmPSMHeaders, splitPSM and cleanupPSM.

Usage

annotPSM(
  group_psm_by = "pep_seq",
  group_pep_by = "prot_acc",
  mc_psm_by = "peptide",
  fasta = NULL,
  expt_smry = "expt_smry.xlsx",
  plot_rptr_int = TRUE,
  plot_log2FC_cv = TRUE,
  rm_allna = FALSE,
  type_sd = "log2_R",
  ...
)

Arguments

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.
mc_psm_by	A character string specifying the method in the median centering of PSM log2FC across samples. At the peptide default, the median description of PSMs (grouped by pep_seq or pep_seq_mod according to group_psm_by) will be first calculated and the offsets to zero (of logarithmic 2) will be used for the centering of PSMs across samples. At mc_psm_by = protein, the median description of PSMs (grouped by prot_acc or gene according to group_pep_by) will be calculated and the corresponding offsets to zero will be applied. At the mc_psm_by = psm, PSMs will be median centered without grouping.
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).
expt_smry	A character string to a .xlsx file containing the metadata of TMT or LFQ experiments. The default is expt_smry.xlsx.
plot_rptr_int	Logical; if TRUE, the distributions of reporter-ion intensities will be plotted. The default is TRUE. The argument is also applicable to the precursor intensity with MaxQuant LFQ.
plot_log2FC_cv	Logical; if TRUE, the distributions of the CV of peptide log2FC will be plotted. The default is TRUE.
rm_allna	Logical; if TRUE, removes data rows that are exclusively NA across ratio columns of log2_R126 etc. The setting also applies to log2_R000 in LFQ.
type_sd	Character string; the type of log2Ratios for SD calculations. The value is one log2_R, N_log2_R or Z_log2_R.
...	Not currently used.

qzhang503/proteoQ documentation built on March 16, 2024, 5:27 a.m.