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According to the documentation, there are eight kinds of plots generated by qQCReport. However, I only see four.
library(QuasR)
testFile <- system.file("extdata", "ex1.bam", package="Rsamtools")
qQCReport(testFile, "testQC.pdf")
Can the function's result be changed to match the documentation? Also, each plot is very small and takes up a small part of a large A4 PDF page, which affects plot legibility. QuasR version 1.22.1 is used.
But the documentation
?qQCReportprovides a list of seven plots which may be generated for any BAM file and an eighth plot which is for BAM files containing paired reads. The test file I used has paired readsSo, I expect to get eight plots but I only get four. Could you run the test code to check how many plots you obtain? The documentation of
qQCReportand its output seems inconsistent.Yes, I agree the documentation is misleading (or even partly wrong). I will talk to the QuasR developers and try to get the documentation improved for of qQCReport.
Hans-Rudolf
Hi Dario
The documentation and also plotting issues have been addressed in QuasR 1.23.17 (will become available in BioC-devel in a day or so).
The documentation has been simplified to make it clear that some plots will not be available if the necessary information is missing (e.g. base quality plots when working with a fasta file). Furthermore,
qQCReportnow has a new argumenta4paper(a4paper = TRUEby default) that allows you to switch off the page-optimised layout for mapping and uniqueness plots.Thank you for your report.
Michael