annotationCoverageAroundFeatures: Extract stranded annotation profiles at and around a set of...

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

Description

Extract stranded annotation profiles at and around a set of features/intervals.

Usage

annotationCoverageAroundFeatures(
  annot,
  features = NULL,
  sidedist = 2000L,
  usePercent = FALSE,
  BinFeatures = TRUE,
  ...
)

Arguments

annot	A GRanges of (stranded) genomic annotations
features	An optional GRanges or a character vector with a subset of annot names to extract profiles at. Defaults to NULL for all annot features.
sidedist	Integer. Distance on each side of features at which to extract the profiles
usePercent	Logical. Should annotation coverage be expressed as presence/absence (0/1)? (instead of counting the number of features aligning at each position)
BinFeatures	Logical. Should features be binned? Default to TRUE and will be forced to TRUE if features have different width.
...	additional arguments passed to binFeatureProfiles

Value

A list with the following elements:

• Feature_Sense: Coverage of annot (possibly binned) at features, on the sense strand (i.e. the strand of the feature)

• Feature_Antisense: Coverage of annot (possibly binned) at features, on the antisense strand (i.e. the opposite strand of features)

• UpstreamBorder_Sense: Coverage of annot around (+/- sidedist) the upstream border of features (Typically the TSS), on the sense strand

• UpstreamBorder_Antisense: Coverage of annot around (+/- sidedist) the upstream border of features, on the antisense strand

• DownstreamBorder_Sense: Coverage of annot around (+/- sidedist) the downstream border of features (Typically the TES), on the sense strand

• DownstreamBorder_Antisense: Coverage of annot around (+/- sidedist) the downstream border of features, on the antisense strand

DETAILS

The usePercent option is intended to give a percentage of bases covered by annotations when performing average profiles from several features.
When calculating a coverage with usePercent=TRUE any value > 1 is replaced by 1.
This is equivalent to calculating coverage(reduce(annot)) instead of coverage(annot).

Author(s)

Pascal GP Martin

See Also

binFeatureProfiles

Examples

## Extract the profiles around (+/-50bp) all genes. We bin the genes in 3 bins only.
AllProf <- annotationCoverageAroundFeatures(Genegr, sidedist = 50, usePercent = TRUE, nbins=3)

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