carpools.waterfall.pval {caRpools}R Documentation

Visualization of p-value distribution

Description

Each of the analysis methods returns an adjusted p-value (corrected for multiple testing) as well as a fold change (Wilcox, DESeq2) or gene rank (MAGeCK). Therefore the -log10 p-value can be plotted against the gene names with 'carpools.waterfall.pval':

Usage

carpools.waterfall.pval (type=NULL,dataset=NULL, pval=0.05, mageck.type="pos", log=TRUE)

Arguments

type

This indicates which kind of analysis method was used for p-value calculation. *Default* NULL *Values* "mageck", "deseq2", "wilcox"

dataset

Result from either 'stat.wilcox', 'stat.DEseq' or 'stat.mageck'. *Default* NULL *Values* Result from either 'stat.wilcox', 'stat.DEseq' or 'stat.mageck'

pval

The significance value set for the analysis which is to be plotted. *Default* 0.05 *Values* numeric

mageck.type

Only for plotting p-value calculate by MAGeCK. Indicates whether enriched ("pos") or depleted ("neg") genes are used. *Default* "pos" *Values* "pos", "neg"

log

-log10 of the p-valiues is plotted if set to TRUE. *Default* TRUE *Values* TRRUE, FALSE (boolean)

Value

Return a generic plot.

Note

none

Author(s)

Jan Winter

Examples

data(caRpools)

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.waterfall.pval(type="mageck", dataset=data.mageck, pval=0.05, log=TRUE)

[Package caRpools version 0.83 Index]