Limma_Adj_pval: Returns adjusted pvalue from decideTests function, instead of...

In Rvirgenslane/Hotgenes: For Visualizing Differential Expression Analysis

Returns adjusted pvalue from decideTests function, instead of -1, 0 or 1

Description

Returns adjusted pvalue from decideTests function, instead of -1, 0 or 1

Usage

Limma_Adj_pval(
  object,
  method = "separate",
  adjust.method = "BH",
  p.value = 0.05,
  lfc = 0
)

Arguments

object	a numeric matrix of p-values or an MArrayLM object from which p-values and t-statistics can be extracted.
method	character string specifying how genes and contrasts are to be combined in the multiple testing scheme. Choices are "separate", "global", "hierarchical" or "nestedF".
adjust.method	character string specifying p-value adjustment method. Possible values are "none", "BH", "fdr" (equivalent to "BH"), "BY" and "holm". See p.adjust for details.
p.value	numeric value between 0 and 1 giving the required family-wise error rate or false discovery rate.
lfc	numeric, minimum absolute log2-fold-change required.

Rvirgenslane/Hotgenes documentation built on June 15, 2024, 2:16 a.m.