Description Usage Arguments Value Examples
This function looks for overlapping exons in ebg
.
The overlapping "genes" are used to form a graph.
Any connected components in the graph (sets of "genes"
which can be reached from each other through overlap relations)
are connected into a new gene cluster, which is given the
suffix "_mrg" and using one of the original gene names.
1 | mergeGenes(ebg, txdf, ignore.strand = TRUE)
|
ebg |
an exons-by-genes GRangesList, created with |
txdf |
a data.frame created by running |
ignore.strand |
Default is TRUE. |
a manipulated txdf
.
1 2 3 4 5 6 7 8 | library(GenomicRanges)
txdf <- data.frame(GENEID=c("101","102","103","104"))
ebg <- GRangesList(GRanges("1",IRanges(c(100,200),width=50)),
GRanges("1",IRanges(c(200,300),width=50)),
GRanges("1",IRanges(c(300,400),width=50)),
GRanges("1",IRanges(c(500,600),width=50)))
names(ebg) <- c("101","102","103","104")
mergeGenes(ebg, txdf)
|
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