ct.makeContrastReport: Generate a Contrast report from a pooled CRISPR screen

In RussBainer/gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Generate a Contrast report from a pooled CRISPR screen

Description

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.

Usage

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

Value

The path to the generated html report.

Author(s)

Russell Bainer, Dariusz Ratman

Examples

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 = '.') 

RussBainer/gCrisprTools documentation built on Nov. 5, 2022, 2:35 p.m.