combine_directional_pvalues: Directionally combine p-values

In jdreyf/jdcbioinfo: Joslin Diabetes Center bioinformatics utilities

Directionally combine p-values

Description

Directionally combine two-sided test p-values.

Usage

combine_directional_pvalues(
  tab,
  prefix.v = NULL,
  p.suffix = "p",
  direction.suffix = "logFC",
  only.p = FALSE,
  prefix = NULL
)

Arguments

tab	Table of output from ezlimma.
prefix.v	A vector of prefixes that prefix .p, .FDR, or .logFC in colnames(tab). These will be the columns that are used in the Venn diagram. If NULL these are inferred from colnames(tab) that end with .p.
p.suffix	The suffix of p-value columns, i.e. the character string after the period "."
direction.suffix	The suffix of direction columns such as log fold-change, regression slope, correlation coefficient, or the "Up/Down" values
only.p	Logical; should only combined p-values be returned? If not, returns matrix with z-scores and FDRs also.
prefix	Character string to add to beginning of column names. NULL does not add a prefix.

Details

prefix.v specifies input column names, whereas prefix is appended to output column names.

Value

Vector of p-values or table with direction, p-values, and FDR.

jdreyf/jdcbioinfo documentation built on April 15, 2024, 6:37 p.m.