caRpools (version 0.83)

carpools.read.depth: 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

Value

plot.read.depth returns a generic plot.

Details

notes

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)