carpools.hit.overview: Analysis: Analysis of pooled CRISPR screening data using a...

Description Usage Arguments Details Value Note Author(s) Examples

Description

Candidate genes from all methods can be plotted in an overview to identify overlapping signficant candidate genes using 'carpools.hit.overview'.

Usage

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carpools.hit.overview(wilcox=NULL, deseq=NULL, mageck=NULL, cutoff.deseq = 0.001,
cutoff.wilcox = 0.05, cutoff.mageck = 0.05, cutoff.override=FALSE, cutoff.hits=NULL,
plot.genes="overlapping", type="all")

Arguments

wilcox

Data output from 'stat.wilcox'. *Default* NULL *Values* Data output from 'stat.wilcox'.

deseq

Data output from 'stat.deseq'. *Default* NULL *Values* Data output from 'stat.deseq'.

mageck

Data output from 'stat.mageck'. *Default* NULL *Values* Data output from 'stat.mageck'.

cutoff.deseq

P-Value threshold used to determine significance. *Default* 0.001 *Values* numeric

cutoff.wilcox

P-Value threshold used to determine significance. *Default* 0.001 *Values* numeric

cutoff.mageck

P-Value threshold used to determine significance. *Default* 0.001 *Values* numeric

cutoff.override

Shall the p-value threshold be ignored? If this is TRUE, the top percentage gene of 'cutoff.hits' is used instead. *Default* FALSE *Values* TRUE, FALSE

cutoff.hits

The percentatge of top genes being used if 'cutoff.override=TRUE'. *Default** NULL *Values* numeric

plot.genes

Defines what kind of data is used. By default, overlapping genes are highlighted in red color. *Default* "overlapping" *Values* "overlapping"

type

Defines whether all genes are plotted or only those being enriched or depleted. *Default* "all" *Values* "all", "enriched", "depleted"

Details

none

Value

Returns a generic plot.

Note

none

Author(s)

Jan Winter

Examples

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data(caRpools)

data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
  treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
  normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
  control.picks=NULL)


data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
  treated.list = list(TREAT1,TREAT2), namecolumn=1,
  fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
  sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
  fitType="parametric")
  
data.mageck = stat.mageck(untreated.list = list(CONTROL1, CONTROL2),
treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
norm.fun="median", extractpattern=expression("^(.+?)(_.+)"),
mageckfolder=NULL, sort.criteria="neg", adjust.method="fdr", filename = "TEST" , fdr.pval = 0.05)

carpools.hit.overview(wilcox=data.wilcox, deseq=data.deseq, mageck=data.mageck,
    cutoff.deseq = 0.001, cutoff.wilcox = 0.05, cutoff.mageck = 0.05,
    cutoff.override=FALSE, cutoff.hits=NULL, plot.genes="overlapping", type="enriched")

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