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RussBainer / gCrisprTools

An R/Bioconductor package for the integrated analysis of pooled high-throughput CRISPR/Cas9 or shRNA screening experiments.
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alignment statistics ct.makeQCReport #16

Closed AMChalkie closed 3 years ago

AMChalkie commented 6 years ago

From https://www.bioconductor.org/packages/devel/bioc/vignettes/gCrisprTools/inst/doc/gCrisprTools_Vignette.html

Code for best practise generation of the aln object would be helpful, commenting on what script/tool usually generates the source matrix.

may => must (in documentation)

2.5 Alignment Statistics Users may provide a matrix of alignment statistics to enhance some applications, including QC reporting. These should be provided as a numeric matrix in which rows correspond to targets (reads containing a target cassette), nomatch (reads containing a cassette sequence but not a known target sequence), rejections (reads not containg a cassette sequence), and double_match (reads derived from multiple cassettes). The column names should exactly match the colnames() of the ExpressionSet object. Simple charting functionality is also provided to inspect the alignment rates of each sample.

ct.makeQCReport(es, trim = 1000, log2.ratio = 0.05, sampleKey = sk, annotation = ann,

aln = aln,

                         identifier = 'Crispr_QC_Report',
                         lib.size = NULL,
                         outdir = file_path_report

)

Error in ct.makeQCReport(es, trim = 1000, log2.ratio = 0.05, sampleKey = sk, : argument "aln" is missing, with no default

RussBainer commented 3 years ago

This has been fixed in the move to 2.0