carpools.read.distribution: QC: Plot Readcount Distribution

In caRpools: CRISPR AnalyzeR for Pooled CRISPR Screens

Description

A distribution for NGS data readcount can be created by 'carpools.read.distribution' to visualize how the data set is distributed. This allows to check for data skewness and to estimate the overall assay quality. For further details see '?carpools.read.distribution'.

Usage

carpools.read.distribution(dataset,namecolumn=1, fullmatchcolumn=2, breaks="",
title="Title", xlab="X-Axis", ylab="Y-Axis",statistics=TRUE,
col=rgb(0, 0, 0, alpha = 0.65), extractpattern=expression("^(.+?)_.+"),
plotgene=NULL, type="distribution", logscale=TRUE)

Arguments

dataset	Data frame of read-count data as created by load.file(). *Default* none *Values* A data 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)
breaks	Histogramm breaks see '?hist'. By default, will be calculated according to the dataset length. *Default* NULL *Values* (numeric)
title	Main title of plot *Default* "Title" *Values* "The title you want" (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)
statistics	Whether basic stattistics will be shown in the plot. *Default* TRUE *Values* TRUE, FALSE (boolean)
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)
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)
plotgene	You can only plot the read count distribution of sgRNAs belonging to a certain gene, which is given to the function via plotgene. *Default* NULL *Value* NULL or gene identifier (character)
type	You can plot either the read count distribution either as a normal histogram, or a box-and-whisker plot. *Default* "distribution" *Values* "distribution" to plot a histogram, or "whisker" to plot a whisker plot (character)
logscale	Indicates whether the read-count is plotted in a logarithmic scale. *Default* TRUE *Values* TRUE, FALSE (boolean)

Details

none

Value

plot.read.distribution return a generic plot, that can be passed on to any device.

Note

none

Author(s)

Jan Winter

Examples

data(caRpools)

carpools.read.distribution(CONTROL1, fullmatchcolumn=2,breaks=200,
  title=d.CONTROL1, xlab="log2 Readcount", ylab="# sgRNAs",statistics=TRUE) 
  
carpools.read.distribution(CONTROL1, fullmatchcolumn=2,breaks=200,
  title=d.CONTROL1, xlab="log2 Readcount", ylab="# sgRNAs",statistics=TRUE,
  type="whisker") 

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