Select_genes: Extracts genes according to logFoldChange and p-val limits

In LauraPS1/TFEA.ChIP: Analyze Transcription Factor Enrichment

Extracts genes according to logFoldChange and p-val limits

Description

Function to extract Gene IDs from a dataframe according to the established limits for log2(FoldChange) and p-value. If possible, the function will use the adjusted p-value column.

Usage

Select_genes(
  GeneExpression_df,
  max_pval = 0.05,
  min_pval = 0,
  max_LFC = Inf,
  min_LFC = -Inf
)

Arguments

GeneExpression_df	A data frame with the folowing fields: 'Gene', 'pvalue' or 'pval.adj', 'log2FoldChange'.
max_pval	maximum p-value allowed, 0.05 by default.
min_pval	minimum p-value allowed, 0 by default.
max_LFC	maximum log2(FoldChange) allowed.
min_LFC	minimum log2(FoldChange) allowed.

Value

A vector of gene IDs.

Examples

data('hypoxia',package='TFEA.ChIP')
Select_genes(hypoxia)

LauraPS1/TFEA.ChIP documentation built on April 21, 2023, 7:29 a.m.