View source: R/generateReports.R
ct.makeReport | R Documentation |
This is a function to generate an html report for a CRISPR screen, incorporating information about a specified contrast.
The report contains a combination of experiment-level and contrast-specific analyses, largely 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.
ct.makeReport(
fit,
eset,
sampleKey,
annotation,
results,
aln,
outdir = NULL,
contrast.term = NULL,
identifier = NULL
)
fit |
An object of class |
eset |
An ExpressionSet object containing, at minimum, a matrix of gRNA abundances extractable with the |
sampleKey |
A sample key, supplied as an ordered factor linking the samples to experimental
variables. The |
annotation |
An annotation object for the experiment. See the man page for |
results |
A data.frame summarizing the results of the screen, returned by the function |
aln |
A numeric alignment matrix, where rows correspond to 'targets', 'nomatch', 'rejections', and 'double_match', and where columns correspond to experimentasl samples. Users may also pass 'NULL' to suppress evaluation of alignment. |
outdir |
A directory in which to generate the report; if |
contrast.term |
A parameter passed to |
identifier |
A character string to name the report and corresponding subdirectories. If provided, the final report will be called
' |
The path to the generated html report.
Russell Bainer
data('fit')
data('es')
##' #Build the sample key
library(Biobase)
sk <- relevel(as.factor(pData(es)$TREATMENT_NAME), 'ControlReference')
names(sk) <- row.names(pData(es))
data('ann')
data('resultsDF')
data('aln')
path2report <- ct.makeReport(fit, es, sk, ann, resultsDF, aln, outdir = '.')
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