getTESregion: Extract a region around the TES (=end of the gene) from a...

In pgpmartin/GeneNeighborhood: Analyze the Neighborhood (Upstream/Downstream Neighbors) of Genes

Description

Extract a region around the TES (=end of the gene) from a GRanges

Usage

getTESregion(
  gr,
  upstream = 500L,
  downstream = 501L,
  limitToTSS = FALSE,
  trim = FALSE
)

Arguments

gr	A GRanges.
upstream	An integer defining the distance upstream of the TES to extract.
downstream	An integer defining the distance downstream of the TES to extract.
limitToTSS	A logical (default to FALSE) indicating if ranges should be trimmed to don't extend upstream of the TSS
trim	A logical (default to FALSE) indicating if out-of-bound ranges should be trimmed (see ?'trim,GenomicRanges-method')

Details

The TES is defined as start(gr) when strand(gr)=="+" and as end(gr) when strand(gr)=="-" The function considers that strand=="*" is equivalent to strand=="+" To extract 500bp on each side of the TES, use upstream=500 and downstream=501

Value

A GRanges of regions around the TES positions.

Author(s)

Pascal GP Martin

See Also

promoters, flank and trim in intra-range-methods getTES

Examples

## Get a 50bp region on each side of the TSS of genes in GeneGR:
  suppressWarnings(
   GenomicRanges::promoters(Genegr,
                              upstream = 50,
                              downstream = 51)
                  )
## Same around the TES:
  suppressWarnings(
    getTESregion(Genegr, upstream = 50, downstream = 51)
    )
## Do not extend regions beyond the TSS or Chr1 borders
  getTESregion(Genegr,
               upstream = 50,
               downstream = 51,
               limitToTSS = TRUE,
               trim = TRUE)

pgpmartin/GeneNeighborhood documentation built on Sept. 2, 2021, 6:37 a.m.