prep_gspa: Helper of GSPA

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

Helper of GSPA

Description

Helper of GSPA

Usage

prep_gspa(
  df,
  id,
  fml_nm,
  col_ind,
  pval_cutoff = 0.05,
  logFC_cutoff = log2(1.2),
  use_adjP = FALSE
)

Arguments

df	The name of a primary data file. By default, it will be determined automatically after matching the types of data and analysis with an id among c("pep_seq", "pep_seq_mod", "prot_acc", "gene"). A primary file contains normalized peptide or protein data and is among c("Peptide.txt", "Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt"). For analyses require the fields of significance p-values, the df will be one of c("Peptide_pVal.txt", "Peptide_impNA_pVal.txt", "Protein_pVal.txt", "protein_impNA_pVal.txt").
id	Currently only "entrez".
fml_nm	A character string; the name of fml.
col_ind	Numeric vector; the indexes of columns for the ascribed fml_nm.
pval_cutoff	Numeric value or vector; the cut-off in protein significance pVal. Entries with pVals less significant than the threshold will be excluded from enrichment analysis. The default is 0.05 for all formulas matched to or specified in argument fml_nms. Formula-specific threshold is allowed by supplying a vector of cut-off values.
logFC_cutoff	Numeric value or vector; the cut-off in protein log2FC. Entries with absolute log2FC smaller than the threshold will be excluded from enrichment analysis. The default magnitude is log2(1.2) for all formulas matched to or specified in argument fml_nms. Formula-specific threshold is allowed by supplying a vector of absolute values in log2FC.
use_adjP	Logical; if TRUE, use Benjamini-Hochberg pVals. The default is FALSE.

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