combineTranscripts {groHMM} | R Documentation |
Combines transcripts that are within the same gene annotation, combining smaller transcripts for genes with low regulation into a single transcript representing the gene.
combineTranscripts(tx, annox, geneSize = 1000, threshold = 0.8, plot = FALSE)
tx |
GRanges of transcripts. |
annox |
GRanges of non-overlapping annotations for reference. |
geneSize |
Numeric. Minimum gene size in annotations to be used as reference. Default: 1000 |
threshold |
Numeric. Ratio of overlapped region relative to transcript width. Transcripts only greater than this threshold are subjected to be combined. Default: 0.8 |
plot |
Logical. If set to TRUE, show easch step in a plot. Default: FALSE |
Returns GRanges object of combined transcripts.
Minho Chae and Charles G. Danko
tx <- GRanges("chr7", IRanges(start=c(1000, 20000), width=c(10000,10000)), strand="+") annox <- GRanges("chr7", IRanges(1000, 30000), strand="+") combined <- combineTranscripts(tx, annox)