makeConsensusAnnotations: makeConsensusAnnotations Makes a consensus annotation

In coregenomics/groHMM: GRO-seq Analysis Pipeline

Description

Makes a non-overlapping consensus annotation. Gene annotations are often overlapping due to #' multiple isoforms for a gene. In consensus annotation, isoforms are first reduced so that only redundant intervals are used to represent a genomic interval for a gene, i.e., a gene id. Remaining unresolved annotations are further reduced by truncating 3' end of annotations.

Usage

makeConsensusAnnotations(ar, minGap = 1L, minWidth = 1000L,
  column = "gene_id", BPPARAM = bpparam())

Arguments

ar	GRanges of annotations to be collapsed.
minGap	Minimum gap between overlapped annotations after truncated. Default: 1L
minWidth	Minimum width of consensus annotations. Default: 1000L
column	Column by which to group transcripts.
BPPARAM	Registered backend for BiocParallel. Default: BiocParallel::bpparam()

Value

Returns GRanges object of annotations.

Author(s)

Minho Chae

Examples

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
tx <- transcripts(
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    columns=c("gene_id", "tx_id", "tx_name"),
    filter=list(tx_chrom="chr7"))
## Workaround Travis-CI issue 7052
if (!is.na(Sys.getenv("TRAVIS", NA)))
    BiocParallel::register(BiocParallel::SerialParam())
ca <- makeConsensusAnnotations(tx)

coregenomics/groHMM documentation built on May 7, 2019, 7:57 a.m.