ct.makeReport: Generate a full experimental report from a pooled CRISPR...
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 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 `MArrayLM` containing, at minimum, a `coefficents` slot with coefficients from the comparison, and a `stdev.unscaled` slot with the corresponding standard deviation of the coefficent estimates. The `row.names` attribute should ideally match that which is found in `annotation`, but this will be checked internally.
`eset`	An ExpressionSet object containing, at minimum, a matrix of gRNA abundances extractable with the `exprs()` function and some named phenodata extractable with `pData()`.
`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.
`results`	A data.frame summarizing the results of the screen, returned by the function `ct.generateResults`.
`aln`	A numeric alignment matrix, where rows correspond to "targets", "nomatch", "rejections", and "double_match", and where columns correspond to experimentasl samples.
`outdir`	A directory in which to generate the report; if `NULL`, a temporary directory will be automatically generated. The report will be located in a subdirectory whose name is internally generated (see below). The path to the report itself is returned by the function.
`contrast.term`	A parameter passed to `ct.preprocessFit` in the event that the fit object contains data from multiple contrasts. See that man page for further details.
`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 including the timestamp will be generated.

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 = ".")