makeConsensusAnnotations {groHMM} | R Documentation |
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.
makeConsensusAnnotations(ar, minGap = 1L, minWidth = 1000L, ...)
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. |
Supports parallel processing using mclapply in the 'parallel' package. To change the number of processors, use the argument 'mc.cores'.
Returns GRanges object of annotations.
Minho Chae
## 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)