mcPSM: Median-centering normalization of PSM data

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

Median-centering normalization of PSM data

Description

mcPSM adds fields of log2_R, N_log2_R and N_I to PSM tables.

Usage

mcPSM(
  df = NULL,
  set_idx = 1L,
  injn_idx = 1L,
  mc_psm_by = "peptide",
  group_psm_by = "pep_seq",
  group_pep_by = "prot_acc",
  rm_allna = FALSE
)

Arguments

df	A data frame containing the PSM table from database searches.
set_idx	Numeric. The index of a multiplex TMT experiment in metadata files such as label_scheme.xlsx and frac_scheme.xlsx.
injn_idx	Numeric. The index of LCMS_Inj in metadata files such as label_scheme.xlsx and frac_scheme.xlsx.
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.
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.
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.

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