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

In TFEA.ChIP: Analyze Transcription Factor Enrichment

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 = NULL, min_LFC = NULL)

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)

TFEA.ChIP documentation built on Nov. 8, 2020, 5:05 p.m.