Generate a QC report from a pooled CRISPR screen

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Description

This is a function to generate an html QC report for a CRISPR screen, focusing on experiment-level and library-level analyses collected from other functions in gCrisprTools. It is designed to be used 'as-is', and analysts interested in using different functionalities of the various functions should do that outside of this wrapper script.

Usage

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ct.makeQCReport(eset, trim, log2.ratio, sampleKey, annotation, aln,
  identifier = NULL, lib.size, geneSymb = NULL, outdir = NULL)

Arguments

eset

An ExpressionSet object containing, at minimum, a matrix of gRNA abundances extractable with the exprs() function and some named phenodata extractable with pData().

trim

The number of gRNAs to be trimmed from the top of the distribution before estimating the abundance range. Empirically, this usually should be equal to about 2 to 5 percent of the guides in the library.

log2.ratio

Maximum abundance of contaminant gRNAs, expressed on the log2 scale from the top of the trimmed range of each sample. That is, log2.ratio = 4 means to discard all gRNAs whose abundance is (1/2)^4 of the trimmed maximum.

sampleKey

A sample key, supplied as an ordered factor linking the samples to experimental variables. The names attribute should exactly match those present in eset, and the control set is assumed to be the first level.

annotation

An annotation object for the experiment. See the man page for ct.prepareAnnotation for details and example format.

aln

A numeric alignment matrix, where rows correspond to "targets", "nomatch", "rejections", and "double_match", and where columns correspond to experimentasl samples.

identifier

A character string to name the report and corresponding subdirectories. If provided, the final report will be called 'identifier.html' and will be located in a directory called identifier. If NULL, a generic name including the timestamp will be generated.

lib.size

An optional vector of voom-appropriate library size adjustment factors, usually calculated with calcNormFactors and transformed to reflect the appropriate library size. These adjustment factors are interpreted as the total library sizes for each sample, and if absent will be extrapolated from the columnwise count sums of the exprs slot of the eset.

geneSymb

The geneSymbol identifier(s) in annotation that corresponds to gRNAs to be plotted on the curves. Passed through to ct.gRNARankByReplicate, ct.viewControls and ct.prepareAnnotation (as controls argument if it's not NULL). Default NULL.

outdir

An optional character string indicating the directory in which to generate the report. If NULL, a temporary directory will be automatically generated.

Value

The path to the generated html report.

Author(s)

Russell Bainer, Dariusz Ratman

Examples

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data('es')
data('ann')
data('aln')

##' #Build the sample key
library(Biobase)
sk <- ordered(relevel(as.factor(pData(es)$TREATMENT_NAME), "ControlReference"))
names(sk) <- row.names(pData(es))

path2report <- ct.makeQCReport(es, trim = 1000, log2.ratio = 0.0625, sk, ann, aln, identifier = NULL, lib.size = NULL, outdir = ".") 

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