ct.gRNARankByReplicate: Visualization of Ranked gRNA Abundances by Replicate

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

Visualization of Ranked gRNA Abundances by Replicate

Description

This function median scales and log2 transforms the raw gRNA count data contained in an ExpressionSet, and then plots the ordered expression values within each replicate. The curve colors are assigned based on a user- specified column of the pData contained in the ExpressionSet. Optionally, this function can plot the location of Nontargeting control guides (or any guides, really) within the distribution.

Usage

ct.gRNARankByReplicate(
  eset,
  sampleKey,
  annotation = NULL,
  geneSymb = NULL,
  lib.size = NULL
)

Arguments

eset	An ExpressionSet object containing, at minimum, count data accessible by exprs() and some phenoData.
sampleKey	A sample key, supplied as a (possibly 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 dataframe indicating the nontargeting controls in the geneID column.
geneSymb	The geneSymbol identifier(s) in annotation that corresponds to gRNAs to be plotted on the curves. If the provided value is not present in the geneSymbol, nontargeting controls will be plotted instead.
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.

Value

A waterfall plot as specified, on the default device.

Author(s)

Russell Bainer

Examples

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.gRNARankByReplicate(es, sk, ann, 'Target1377')

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