assembleProfiles: Assemble profiles from the results of the...

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

Description

Assemble profiles from the results of the annotationCoverageAroundFeatures function.
For each gene/feature, the function creates a profile containing:

1. A region upstream of the feature ending with the upstream border of the feature (typically the TSS)

2. A region covering the body of the feature (possibly binned to normalize for different features' sizes)

3. A region downstream of the feature starting with the downstream border of the feature (typically the TES)

Usage

assembleProfiles(annotcovr, sideDist = NULL)

Arguments

annotcovr

a list with 6 RleLists named: Feature_Sense: Coverage (possibly binned) on the body of features, on the sense strand (i.e. the strand of the feature) Feature_Antisense: Coverage (possibly binned) on the body of features, on the antisense strand (i.e. the opposite strand of features) UpstreamBorder_Sense: Coverage centered on the upstream border of features (Typically the TSS), on the sense strand UpstreamBorder_Antisense: Coverage centered on the the upstream border of features, on the antisense strand DownstreamBorder_Sense: Coverage centered on the downstream border of features (Typically the TES), on the sense strand DownstreamBorder_Antisense: Coverage centered on the the downstream border of features, on the antisense strand as produced by the annotationCoverageAroundFeatures function

sideDist

Integer (optional). Distance to keep on each side of the features. Defaults to the maximum distance availabe in annotcovr

Value

a list of 2 RleLists corresponding to:

• Profiles_Sense: RleList of profiles for the sense strand

• Profiles_Antisense: RleList of profiles for the antisense strand

See Also

annotationCoverageAroundFeatures

Examples

## Extract the profiles around (+/-50bp) the first 10 genes. We bin the genes in 3 bins only.
  top10Prof <- annotationCoverageAroundFeatures(Genegr, features=1:10,
                                                sidedist = 50,
                                                usePercent = TRUE,
                                                nbins=3)
## Assemble the profiles:
  Prof <- assembleProfiles(top10Prof)

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