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")