gspa_summary_limma: GSPA pVal calculations using limma

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

GSPA pVal calculations using limma

Description

GSPA pVal calculations using limma

Usage

gspa_summary_limma(
  gset,
  df,
  min_size = 10,
  min_delta = 4,
  gspval_cutoff = 0.05,
  gslogFC_cutoff = 1.2
)

Arguments

gset	Character string; a gene set indicated by gset_nms.
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").
min_size	Numeric value or vector; minimum number of protein entries for consideration in gene set tests. The number is after data filtration by pval_cutoff, logFC_cutoff or varargs expressions under filter_. The default is 10 for all formulas matched to or specified in argument fml_nms. Formula-specific threshold is allowed by supplying a vector of sizes.
min_delta	Numeric value or vector; the minimum count difference between the up- and the down-expressed group of proteins for consideration in gene set tests. For example at min_delta = 4, a gene set will 6 upregulated proteins and 2 down-expressed proteins, or vice versa, will be assessed. The number is after data filtration by pval_cutoff, logFC_cutoff or varargs expressions under filter_. The default is 4 for all formulas matched to or specified in argument fml_nms. Formula-specific threshold is allowed by supplying a vector of sizes.
gspval_cutoff	Numeric value or vector; the cut-off in gene-set significance pVal. Only enrichment terms with pVals more significant than the threshold will be reported. 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.
gslogFC_cutoff	Numeric value or vector; the cut-off in gene-set enrichment fold change. Only enrichment terms with absolute fold change greater than the threshold will be reported. 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.

qzhang503/proteoQ documentation built on April 13, 2025, 8:31 a.m.