ct.makeReport {gCrisprTools} | R Documentation

## Generate a full experimental report from a pooled CRISPR screen

### Description

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.

### Usage

    ct.makeReport(
      fit,
      eset,
      sampleKey,
      annotation,
      results,
      aln,
      outdir = NULL,
      contrast.term = NULL,
      identifier = NULL
    )

### Arguments

`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.

### Value

The path to the generated html report.

### Author(s)

Russell Bainer

### Examples

    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 = ".")

[Package gCrisprTools version 1.18.0 Index]