summarizeOverlapsWithFeatureList: Summarize overlaps with a feature list

In AdrijaK/omicsWrappers: wrapper functions for integrating and visualising ChIPseq, ATACseq, Hi-C, pcHi-C and RNAseq data

Description

counts overlaps between a GRanges object (query) in each item of GRangesList (many subjects) outputs the count of overlaps for each GRanges element as a data frame

Usage

summarizeOverlapsWithFeatureList(GRanges_query, GRangesList_subject)

Arguments

GRanges_query	GRanges object that will be used as a query
GRangesList_subject	GRangesList object that will be used as a subject

Value

GRanges_query with overlaps from each item in GRangesList_object as a column in mcols()

Examples

# make a features list from snakePipes chip-seq pipeline output
featuresList = makeFeaturesList("/scratch/adrija/02_MLL/data/chip-seq/DNA-mapping/CSAW_MACS2_CEBPa")

# make a GRanges query from ATAC peaks
ATAC_peaks = omicsWrappers::loadBed6AsGRanges("/localhome/bric/qlr900/analysis/02_MLL/data/atac/DNA-mapping/CSAW_MACS2_ATAC/DiffBinding_allregions.bed")

summarize overlaps
summarizeOverlapsWithFeatureList(ATAC_peaks, featuresList)

AdrijaK/omicsWrappers documentation built on July 22, 2020, 2:11 p.m.