getTADOverlap: For given region of interest, overlapped genes in the TAD...

In guldenolgun/NoRCE: NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

For given region of interest, overlapped genes in the TAD regions are found. Results can be filtered according to the available cell lines.

Description

For given region of interest, overlapped genes in the TAD regions are found. Results can be filtered according to the available cell lines.

Usage

getTADOverlap(
  bedfile,
  org_assembly = c("hg19", "hg38", "mm10", "dre10", "rn6", "dm6", "ce11", "sc3"),
  tad = c(tad_hg19, tad_dmel, tad_hg38, tad_mm10),
  near = FALSE,
  upstream = 10000,
  downstream = 10000,
  cellline = "all"
)

Arguments

bedfile	Region of interest
org_assembly	Genome assembly of interest for the analysis. Possible assemblies are "mm10" for mouse, "dre10" for zebrafish, "rn6" for rat, "dm6" for fruit fly, "ce11" for worm, "sc3" for yeast, "hg19" and "hg38" for human
tad	TAD genomic regions for the species. Predefined TAD regions or any new TAD regions can be used for the analysis. TAD regions must be formated as GRanges object. Predefined TAD regions are 'tad_hg19', 'tad_hg38', 'tad_mm10', 'tad_dmel' for hg19, hg38, mm9 and dm6 assembly, respectively.
near	Boolean value presents whether cis-neighbourhood should be considered in the analysis
upstream	Holds upstream distance from the transcription start position
downstream	Holds downstream distance from the transcription end position
cellline	Cell lines for TAD regions.

Value

List of protein coding genes that falls into the TAD regions

Examples

## Not run: 
regions<-system.file("extdata", "ncRegion.txt", package = "NoRCE")
regionNC <- rtracklayer::import(regions, format = "BED")

r<-getTADOverlap(bedfile = regionNC,
                 tad = tad_hg19,
                 org_assembly = 'hg19',
                 cellline = 'HUVEC')

## End(Not run)

guldenolgun/NoRCE documentation built on Oct. 21, 2022, 11:48 a.m.