View source: R/rearlist-utils.R
seqJunctions_Rlist | R Documentation |
This function constructs a GRanges
object of the 5-prime and 3-prime sequence junctions for a RearrangementList
that has already been ordered by its two 5-prime to 3-prime orientation.
seqJunctions_Rlist(rlist)
rlist |
a |
a GRanges
object of the 5-prime and 3-prime sequence junctions. The 3-prime junctions are included in the '3p' field of the GRanges
object
library(trellis) extdata <- system.file("extdata", package="svbams") rfile <- file.path(extdata, "CGOV11T_1.bam.rds") rlist <- readRDS(rfile) near.coding <- seqJunctionNearTx(rlist, "hg19") ## Just do the first two index <- which(near.coding)[1:2] rlist2 <- fiveTo3List(rlist[index], build="hg19") jxns <- seqJunctions_Rlist(rlist2) jxns
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