caRpools (version 0.83)

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

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)

Value

carpools.reads.genedesigns returns a generic plot.

Details

none

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")