plotOverlapsWithFeaturesList: a wrapper function that plots promoter (GRanges) overlaps...

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

Description

1. count overlaps for each element in GRanges with features stored in GRangesList_subject using summarizeOverlapsWithFeatureList

2. group the mcols of GRanges by status (DOWN/None/UP -regulated)

3. normalise the counts against the number of genes per group and express that as percentage

4. subset the peaks_none, peaks_up, peaks_down and convert to long format for ggplot

Usage

plotOverlapsWithFeaturesList(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

Details

plotFeatureOverlaps

Examples

  CEBPa = makeFeaturesList("/localhome/bric/qlr900/analysis/02_MLL/data/chip-seq/DNA-mapping/CSAW_MACS2_CEBPa")
  expressedGenes =  allGenes %>% subset(baseMean > 10)
  find coordinates of promoters of deregulated genes:
   promoters_of_expressedGenes =  left_join(expressedGenes, promoters_GRCm38_M24_basic, by = c("geneID" = "gene_id")) %>% as("GRanges")
# use encode_GRCm38_M24_basic for to make annotation
txdb =
  makeTxDbFromGFF("/scratch/genomes/snakepipes/GRCm38_M24_basic/annotation/genes.gtf",
                  format=c("gtf"),
                  dataSource="gencode_GRCm38_M24_basic")

promoters_GRCm38_M24_basic = genes(txdb) %>% promoters %>% as.data.frame
plotOverlapsWithFeaturesList (promoters_of_expressedGenes, CEBPa)

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