preprocessInputData: Extracts data from a DESeqResults object or a data frame.

In LauraPS1/TFEA.ChIP: Analyze Transcription Factor Enrichment

Extracts data from a DESeqResults object or a data frame.

Description

Function to extract Gene IDs, logFoldChange, and p-val values from a DESeqResults object or data frame. Gene IDs are translated to ENTREZ IDs, if possible, and the resultant data frame is sorted accordint to decreasing log2(Fold Change). Translating gene IDs from mouse to their equivalent human genes is avaible using the variable "mode".

Usage

preprocessInputData(inputData, mode = "h2h")

Arguments

inputData	DESeqResults object or data frame. In all cases must include gene IDs. Data frame inputs should include 'pvalue' and 'log2FoldChange' as well.
mode	Specify the organism used: 'h2h' for homo sapiens gene IDs, 'm2m' for mouse gene IDs, or 'm2h' to get the corresponding human gene IDs from a mouse input.

Value

A table containing Entrez Gene IDs, LogFoldChange and p-val values (both raw p-value and fdr adjusted p-value), sorted by log2FoldChange.

Examples

data('hypoxia_DESeq',package='TFEA.ChIP')
preprocessInputData( hypoxia_DESeq )

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