genebodies: Extract Genebodies

In BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data

Description

This function returns ranges that are defined relative to the strand-specific start and end sites of regions of interest (usually genes).

Usage

genebodies(
  genelist,
  start = 300,
  end = -300,
  fix.start = "start",
  fix.end = "end",
  min.window = 0
)

Arguments

genelist	A GRanges object containing genes of interest.
start	Depending on fix.start, the distance from either the strand-specific start or end site to begin the returned ranges. If positive, the returned range will begin downstream of the reference position; negative numbers are used to return sites upstream of the reference. Set start = 0 to return the reference position.
end	Identical to the start argument, but defines the strand-specific end position of returned ranges. end must be downstream of start.
fix.start	The reference point to use for defining the strand-specific start positions of returned ranges, either "start" or "end".
fix.end	The reference point to use for defining the strand-specific end positions of returned ranges, either "start" or "end". Cannot be set to "start" if fix.start = "end".
min.window	When fix.start = "start" and fix.end = "end", min.window defines the minimum size (width) of a returned range. However, when fix.end = fix.start, all returned ranges have the same width, and min.window simply size-filters the input ranges.

Details

Unlike GenomicRanges::promoters, distances can be defined to be upstream or downstream by changing the sign of the argument, and both the start and end of the returned regions can be defined in terms of the strand-specific start or end site of the input ranges. For example, genebodies(txs, -50, 150, fix.end = "start") is equivalent to promoters(txs, 50, 151) (the downstream edge is off by 1 because promoters keeps the downstream interval closed). The default arguments return ranges that begin 300 bases downstream of the original start positions, and end 300 bases upstream of the original end positions.

Value

A GRanges object that may be shorter than genelist due to filtering of short ranges. For example, using the default arguments, genes shorter than 600 bp would be removed.

Author(s)

Mike DeBerardine

See Also

intra-range-methods

Examples

data("txs_dm6_chr4") # load included transcript data
txs <- txs_dm6_chr4[c(1, 2, 167, 168)]

txs

#--------------------------------------------------#
# genebody regions from 300 bp after the TSS to
# 300 bp before the polyA site
#--------------------------------------------------#

genebodies(txs, 300, -300)

#--------------------------------------------------#
# promoter-proximal region from 50 bp upstream of
# the TSS to 100 bp downstream of the TSS
#--------------------------------------------------#

promoters(txs, 50, 101)

genebodies(txs, -50, 100, fix.end = "start")

#--------------------------------------------------#
# region from 500 to 1000 bp after the polyA site
#--------------------------------------------------#

genebodies(txs, 500, 1000, fix.start = "end")

BRGenomics documentation built on Nov. 8, 2020, 8:03 p.m.