get_significant_terms: Get significant term list

In wulingyun/CopTea: Combinatorial OPTimization based Enrichment Analysis

Description

Extract and rank the significant terms with p-values smaller than the given threshold.

Usage

get_significant_terms(
  p.values,
  term.info,
  threshold = 0.05,
  filters = NULL,
  z.score = NULL,
  adjust.p = "bonferroni"
)

Arguments

p.values	The vector of p-values.
term.info	The matrix of term information with three columns: Term ID, Term category, and Term description. The row names should be set as Term ID. See get_annotations for more information.
threshold	The threshold of significant p-value.
filters	The vector of term categories for filtering terms. Set NULL to disable filter.
z.score	The vector of Z-scores associated with p-values, used to sort the terms of same p-values.
adjust.p	The method for adjusting p-values for multiple testing. Use "none" for bypassing. See p.adjust for available methods.

Value

This function returns a matrix with four columns: Rank, Term ID, Term category, and Term description.

See Also

get_annotations

wulingyun/CopTea documentation built on Dec. 4, 2019, 2:59 p.m.