carpools.reads.genedesigns: QC: Plot representation of sgRNAs per gene

In caRpools: CRISPR AnalyzeR for Pooled CRISPR Screens

Description

Since in most cases several sgRNAs are used to target a gene, the information how many sgRNAs are present in the data for each gene is of interest to make sure the number of sgRNAs present is still sufficient. Typically, only few sgRNAs should get "lost" during the screening procedure, so that the full sgRNA coverage is maintained throughout the assay. The only exception would be drop-out screens with a stringent setup. The representation of sgRNAs per gene can be plotted using 'carpools.reads.genedesigns'. For further details see '?carpools.reads.genedesigns'.

Usage

carpools.reads.genedesigns(dataset, namecolumn=1, fullmatchcolumn=2, title="Read Count",
xlab="Percentage of sgRNAs present", ylab="Number of Genes", agg.function=sum,
extractpattern=expression("^(.+?)_.+"), col = rgb(0, 0, 0, alpha = 0.65))

Arguments

dataset	A data frame of read-count data as created by load.file(). *Default* none *Values* Adata frame
namecolumn	In which column are the sgRNA identifiers? *Default* 1 *Values* column number (numeric)
fullmatchcolumn	In which column are the read counts? *Default* 2 *Values* column number (numeric)
title	The title of the plot. *Default* "Read Count" *Values* "Any title" (character)
xlab	Label of X-Axis *Default* "X-Axis" *Values* "Label of X-Axis" (character)
ylab	Label of Y-Axis *Default* "Y-Axis" *Values* "Label of Y-Axis" (character)
agg.function	The function to aggregate sgRNA read-count. *Default* sum *Values* any mathematical function (function)
extractpattern	PERL regular expression that is used to retrieve the gene identifier from the overall sgRNA identifier. e.g. in **AAK1_107_0** it will extract **AAK1**, since this is the gene identifier beloning to this sgRNA identifier. **Please see: Read-Count Data Files** *Default* expression("^(.+?)(_.+)"), will work for most available libraries. *Values* PERL regular expression with parenthesis indicating the gene identifier (expression)
col	The color of the plotted data. Can be any R color or RGB object. See ?rgb() for further information. *Default* rgb(0, 0, 0, alpha = 0.65) *Values* Any R color name or RGB color object (character OR color object)

Details

none

Value

carpools.reads.genedesigns returns a generic plot.

Note

none

Author(s)

Jan Winter

Examples

data(caRpools)

control1.readspergene = carpools.reads.genedesigns(CONTROL1, namecolumn=1, fullmatchcolumn=2,
title=paste("sgRNA Represenation:", d.CONTROL1, sep=" "),
xlab="Percentage of sgRNAs present", ylab="# of Genes")

caRpools documentation built on May 2, 2019, 11:26 a.m.