plotSpliceSum {ggbio} | 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
## 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)