caRpools (version 0.83)

carpools.raw.genes: Plotting sgRNA phenotype effects of a given gene

Description

CaRpools also allows you to visualize the phenotypic effects of sgRNA belonging to the same gene via `carpools.raw.genes`. This includes plotting of sgRNA foldchanges, z-score, z-ratios or read-counts. Moreover, `type="vioplot"` will present fold change data in comparison to the whole dataset and controls.

Usage

carpools.raw.genes(untreated.list,treated.list, genes=NULL, namecolumn=1,
fullmatchcolumn=2, norm.function=median, extractpattern=expression("^(.+?)_.+"),
do.plot=TRUE, log=FALSE, put.names=FALSE, type="foldchange", controls.target= NULL,
controls.nontarget=NULL, sort=TRUE)

Arguments

untreated.list

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

treated.list

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

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)

norm.function

The mathematical function to normalize data if `normalize=TRUE`. By default, the median is used. *Default* median *Values* Any mathematical function of R (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)

do.plot

Whether a plot is drawn or only tabular output is returned. *Default* TRUE *Values* TRUE, FALSE (boolean)

log

Plot in log-scale? *Default* FALSE *Values* TRUE, FALSE (boolean)

put.names

Do you want the sgRNA identifiers to be plotted? *Default* FALSE *Values* TRUE, FALSE

type

Provides different types. "foldchange" for log2 foldchange, "readcount" for read-count, "z-score" for Z-scores, "z-ratio" for a Z-ratio or "vioplot" for a log2 FC of sgRNA effects. *Default* "foldchange" *Values* "foldchange", "readcount", "z-score", "z-ratio", "vioplot"

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)

sort

This leads to output sorted by foldchange or z-ratio instead of names. *Default* TRUE *Values* TRUE, FALSE

genes

For which gene shall the sgRNA effect plots being generated?

Value

Return either generic plots or tables.

Details

none

Examples

data(caRpools)

# Foldchange
p1 = carpools.raw.genes(untreated.list = list(CONTROL1, CONTROL2),
  treated.list = list(TREAT1, TREAT2), genes="CASP8", namecolumn=1,
  fullmatchcolumn=2, norm.function=median, extractpattern=expression("^(.+?)_.+"), 
  do.plot=TRUE, log=FALSE, put.names=TRUE, type="foldchange" )

# Z-Ratio
p2 = carpools.raw.genes(untreated.list = list(CONTROL1, CONTROL2),
  treated.list = list(TREAT1, TREAT2), genes="CASP8", namecolumn=1,
  fullmatchcolumn=2, norm.function=median, extractpattern=expression("^(.+?)_.+"), 
  do.plot=TRUE, log=FALSE, put.names=TRUE, type="z-ratio" )

# Read Count
p3 = carpools.raw.genes(untreated.list = list(CONTROL1, CONTROL2),
  treated.list = list(TREAT1, TREAT2), genes="CASP8", namecolumn=1,
  fullmatchcolumn=2, norm.function=median, extractpattern=expression("^(.+?)_.+"), 
  do.plot=TRUE, log=FALSE, put.names=TRUE, type="readcount" )

# Violine plot
p4 = carpools.raw.genes(untreated.list = list(CONTROL1, CONTROL2),
  treated.list = list(TREAT1, TREAT2), genes="CASP8", namecolumn=1,
  fullmatchcolumn=2, norm.function=median, extractpattern=expression("^(.+?)_.+"), 
  do.plot=TRUE, log=FALSE, put.names=TRUE, type="vioplot" )