makeConsensusAnnotations: makeConsensusAnnotations Makes a consensus annotation

In groHMM: GRO-seq Analysis Pipeline

Description

Makes a non-overlapping consensus annotation. Gene annotations are often overalpping 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, ...)

Arguments

ar	GRanges of annotations to be collapsed.
minGap	Minimun gap between overlapped annotations after truncated. Default: 1L
minWidth	Minimun width of consensus annotations. Default: 1000L
...	Extra argument passed to mclapply.

Details

Supports parallel processing using mclapply in the 'parallel' package. To change the number of processors, use the argument 'mc.cores'.

Value

Returns GRanges object of annotations.

Author(s)

Minho Chae

Examples

## Not run:
# library(TxDb.Hsapiens.UCSC.hg19.knownGene)
# txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
# tx <- transcripts(txdb, columns=c("gene_id", "tx_id", "tx_name"),
#                         filter=list(tx_chrom="chr7"))
# tx <- tx[grep("random", as.character(seqnames(tx)), invert=TRUE),]
# ca <- makeConsensusAnnotations(tx)

groHMM documentation built on Nov. 8, 2020, 8:09 p.m.