ct.viewControls: View nontargeting guides within an experiment
In gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Description Usage Arguments Value Author(s) Examples

This function tries to identify, and then plot the abundance of, the full set of non-targeting controls from an ExpressionSet object. Ideally, the user will supply a geneSymbol present in the appropriate annotation file that uniquely identifies the nontargeting gRNAs. Absent this, the the function will search for common identifier used by nontargeting controls (geneID "no_gid", or geneSymbol NA).

ct.viewControls(
  eset,
  annotation,
  sampleKey,
  geneSymb = NULL,
  normalize = TRUE,
  lib.size = NULL
)

`eset`	An ExpressionSet object containing, at minimum, a matrix of gRNA abundances extractable with the `exprs` function.
`annotation`	An annotation data.frame for the experiment. gRNAs are annotated by row, and must minimally contain columns `geneSymbol` and `geneID`.
`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 condition is assumed to be the first `level`.
`geneSymb`	The `geneSymbol` identifier in `annotation` that corresponds to nontargeting gRNAs. If absent, `ct.ViewControls` will attempt to infer nontargeting guides by searching for `"no_gid"` or `NA` in the appropriate columns.
`normalize`	Logical indicating whether to attempt to normalize the data in the `eset` by DESeq size factors present in the metadata. If `TRUE`, then the metadata must contain a column containing these factors, named `sizeFactor.crispr-gRNA`.
`lib.size`	An optional vector of voom-appropriate library size adjustment factors, usually calculated with `calcNormFactors` and transformed to reflect the appropriate library size. These adjustment factors are interpreted as the total library sizes for each sample, and if absent will be extrapolated from the columnwise count sums of the `exprs` slot of the `eset`.

An image of nontargeting control gRNA abundances on the default device.

Russell Bainer

data('es')
data('ann')

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

ct.viewControls(es, ann, sk, geneSymb = NULL, normalize = FALSE)
ct.viewControls(es, ann, sk, geneSymb = NULL, normalize = TRUE)