extractRegions: extract significant regions

In EMBL-Hentze-group/DEWSeq: Differential Expressed Windows Based on Negative Binomial Distribution

extract significant regions

Description

extract significant windows from output of resultsDEWSeq using the supplied padj and log2FoldChange cut-offs and merge these significant windows to regions and create the following columns for each significant region:

• padj_min: min. padj value in the region

• padj_mean: average padj value in the region

• padj_max: max. padj value in the region

• log2FoldChange_min: min. log 2 fold change in the region

• log2FoldChange_mean: average log 2 fold change in the region

• log2FoldChange_max: max. log 2 fold change in the region

Usage

extractRegions(
  windowRes,
  padjCol = "padj",
  padjThresh = 0.05,
  log2FoldChangeCol = "log2FoldChange",
  log2FoldChangeThresh = 1,
  start0based = TRUE
)

Arguments

windowRes	data.frame, output from resultsDEWSeq
padjCol	character, name of the adjusted pvalue column (default: padj)
padjThresh	numeric, threshold for p-adjusted value (default: 0.05)
log2FoldChangeCol	character, name of the log2foldchange column (default: log2FoldChange)
log2FoldChangeThresh	numeric, threshold for log2foldchange value (default:1)
start0based	logical, TRUE (default) or FALSE. If TRUE, then the start positions in windowRes is considered to be 0-based

Details

The output data.frame from this function will have the following columns:

• chromosome: chromosome name

• regionStartId: unique_id of the left most window, where an enriched region begins

• region_begin: starting position of the enriched region

• region_end: ending position of the enriched region

• strand: strand info

• windows_in_region: total number of windows that make up the enriched region

• region_length: length of the enrched region

• gene_id: gene id

• gene_name: gene name

• gene_type: gene type annotation

• gene_region: gene region

• Nr_of_region: number of the current region

• Total_nr_of_region: total number of regions

• window_number: window number

• padj_min: min. padj value in the region

• padj_mean: average padj value in the region

• padj_max: max. padj value in the region

• log2FoldChange_min: min. log 2 fold change in the region

• log2FoldChange_max: max. log 2 fold change in the region

• log2FoldChange_mean: average log 2 fold change in the region

Value

data.frame

Examples

data("slbpWindows")
# using default cut-off thresholds,
# 'pSlidingWindows.adj' padj value columns
slbpRegions <- extractRegions(slbpWindows,
padjCol = 'pSlidingWindows.adj')

EMBL-Hentze-group/DEWSeq documentation built on Oct. 17, 2023, 10:41 p.m.