groHMM (version 1.6.0)

makeConsensusAnnotations: makeConsensusAnnotations Makes a consensus annotation

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.

Value

Returns GRanges object of annotations.

Details

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

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)