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

In caRpools: CRISPR AnalyzeR for Pooled CRISPR Screens

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?

Details

none

Value

Return either generic plots or tables.

Note

none

Author(s)

Jan Winter

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" )

Example output

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