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

View source: R/getNearest.R

getTADOverlapR Documentation

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.