plotSpliceEvent {ribosomeProfilingQC} | R Documentation |
Plot the splice event
plotSpliceEvent( se, tx_name, coverage, group1, group2, cutoffFDR = 0.05, resetIntronWidth = TRUE )
se |
Output of spliceEvent |
tx_name |
Transcript name. |
coverage |
Coverages of feature region with extensions. Output of coverageDepth |
group1, group2 |
The sample names of group 1 and group 2 |
cutoffFDR |
Cutoff of FDR |
resetIntronWidth |
logical(1). If set to true, reset the region with no read to minimal width. |
A ggplot object.
## Not run: path <- system.file("extdata", package="ribosomeProfilingQC") RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE) gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz") coverage <- coverageDepth(RPFs, gtf=gtf, level="gene", region="feature with extension") group1 <- c("RPF.KD1.1", "RPF.KD1.2") group2 <- c("RPF.WT.1", "RPF.WT.2") se <- spliceEvent(coverage, group1, group2) plotSpliceEvent(se, se$feature[1], coverage, group1, group2) ## End(Not run)