ct.makeContrastReport: Generate a Contrast report from a pooled CRISPR screen
In gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Description Usage Arguments Value Author(s) Examples

This is a function to generate an html Contrast report for a CRISPR screen, focusing on contrast-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.

ct.makeContrastReport(
  eset,
  fit,
  sampleKey,
  results,
  annotation,
  comparison.id,
  identifier,
  contrast.subset = colnames(eset),
  outdir = NULL
)

`eset`	An ExpressionSet object containing, at minimum, a matrix of gRNA abundances extractable with the `exprs()` function and some named phenodata extractable with `pData()`.
`fit`	A fit object for the contrast of interest, usually generated with `lmFit`.
`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`.
`results`	A data.frame summarizing the results of the screen, returned by the function `ct.generateResults`.
`annotation`	An annotation object for the experiment. See the man page for `ct.prepareAnnotation()` for details and example format.
`comparison.id`	character with a name of the comparison.
`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` in the `outdir`. If `NULL`, a generic name
`contrast.subset`	character vector containing the sample labels to be used in the analysis; all elements must be contained in the `colnames` of the specified `eset`. including the timestamp will be generated. Default: `colnames(eset)`.
`outdir`	An optional character string indicating the directory in which to generate the report. If `NULL`, a temporary directory will be automatically generated.

The path to the generated html report.

Russell Bainer, Dariusz Ratman

data('es')
data('fit')
data('ann')
data('resultsDF')

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

path2report <- ct.makeContrastReport(es, fit, sk, resultsDF, ann, comparison.id = NULL, outdir = ".")