caRpools (version 0.83)

generate.hits: Retrieving overlapping hits from caRpools analysis

Description

CaRpools can also calculate which genes overlapped in all hit analysis methods using `generate.hits`.

Usage

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

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 returned, by default only overlapping genes or MAGeCK. *Default* "overlapping" *Values* "overlapping"

type

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

Value

generate.hits return a vector with overlapping candidate genes from all analysis methods.

Details

none

Examples

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)

overlap.enriched = generate.hits(wilcox=data.wilcox, deseq=data.deseq,
mageck=data.mageck, type="enriched", cutoff.deseq = 0.001, cutoff.wilcox = 0.05,
cutoff.mageck = 0.05, cutoff.override=FALSE, cutoff.hits=NULL, plot.genes="overlapping")
print(overlap.enriched)