plotSpliceSum | R Documentation |
Plot splice summary by simply counting overlaped junction read in weighted way or not.
## For character,GRangesList
## S4 method for signature 'character,GRangesList'
plotSpliceSum(data, model, ..., weighted = TRUE)
## For character,TxDb
## S4 method for signature 'character,TxDb'
plotSpliceSum(data, model, which,
..., weighted = TRUE)
## For character,EnsDb
## S4 method for signature 'character,EnsDb'
plotSpliceSum(data, model, which,
..., weighted = TRUE)
data |
A character specifying the bam file path of RNA-seq data. |
model |
A GRangesList which represting different isoforms, a TxDb or an
|
which |
A GRanges object specifying the region you want to get model from
the TxDb object.
For |
weighted |
If |
... |
Extra arugments passed to |
Internally we use biovizBase:::spliceSummary for simple counting, but
we encourage users to use their own robust way to make slicing summary
and store it as GRangesList, then plot the summary by qplot
function.
A ggplot object.
Tengfei Yin
qplot
## Not run:
bamfile <- system.file("extdata", "SRR027894subRBM17.bam", package="biovizBase")
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
data(genesymbol)
exons <- exonsBy(txdb, by = "tx")
exons.rbm17 <- subsetByOverlaps(exons, genesymbol["RBM17"])
plotSpliceSum(bamfile, exons.rbm17)
plotSpliceSum(bamfile, exons.rbm17, weighted = FALSE, offset = 0.01)
plotSpliceSum(bamfile, txdb, which = genesymbol["RBM17"])
plotSpliceSum(bamfile, txdb, which = genesymbol["RBM17"], offset = 0.01)
plotSpliceSum(bamfile, txdb, which = genesymbol["RBM17"],
show.label = TRUE,
label.type = "count")
## End(Not run)
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