makeConsensusAnnotations Makes a consensus annotation

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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

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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

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## 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)

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