carpools.read.depth {caRpools}R Documentation

QC: Plot Sequencing Read Depth

Description

You can also visualize the read depth of genes per sgRNA in order to check for sufficient sequencing depth using 'carpools.read.depth'. For further details see '?carpools.read.depth'. You can either plot single dat samples or all four data samples at once.

Usage

carpools.read.depth(datasets, namecolumn=1, fullmatchcolumn=2, dataset.names=NULL,
extractpattern=expression("^(.+?)_.+"), col=rgb(0, 0, 0, alpha = 0.65), xlab="Genes",
ylab="Read Count per sgRNA", statistics=TRUE, labelgenes = NULL,
controls.target = controls.target,
controls.nontarget=controls.nontarget, labelcolor="orange", waterfall=FALSE)

Arguments

datasets

A list of data frames of read-count data as created by load.file(). *Default* none *Values* A list of data frames

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)

dataset.names

A list of names that must be according to the list of data sets given in *dataset*. *Default* NULL *Value* NULL or list of data names (list)

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)

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)

labelgenes

You can highlight certain genes within the plot. This expects a gene identifier or a fector of gene identifiers. *Default* NULL *Values* A gene identifier or vector of gene identifiers (character)

labelcolor

Color to highlight genes stated in 'labelgenes'. *Default* "organge" *Values* Any R color or RGB color object.

controls.target

Highlights the positive control in red color. *Default* NULL *Value* Gene Identifier (character)

controls.nontarget

Highlights the non-targeting control in blue color. *Default* "random" *Value* Gene Identifier (character)

waterfall

You can either plot the read depth sorted by gene identifier (FALSE, default) or according to the read depth. *Default* FALSE *Values* TRUE, FALSE (boolean) s

Details

notes

Value

plot.read.depth returns a generic plot.

Note

none

Author(s)

Jan Winter

Examples

data(caRpools)

carpools.read.depth(datasets = list(CONTROL1), namecolumn=1 ,fullmatchcolumn=2,
  dataset.names=list(d.CONTROL1), extractpattern=expression("^(.+?)_.+"),
  xlab="Genes", ylab="Read Count per sgRNA",statistics=TRUE, labelgenes = NULL,
  controls.target = "CASP8", controls.nontarget="random", waterfall=FALSE)


[Package caRpools version 0.83 Index]