makeConsensusAnnotations {groHMM} | R Documentation

## 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.

### 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)

[Package groHMM version 1.20.0 Index]