screenMatch: Matching the gene annotation of two screens

In cellHTS: Analysis of cell-based screens

Description

Match the annotation of two cellHTS objects in order to find the common gene-perturbing reagents

Usage

screenMatch(screens, ids)

Arguments

screens	a list of annotated cellHTS objects.
ids	a character vector of length two giving, for each cellHTS object, the name of the column of slot 'geneAnno' that should be used for the annotation IDs. See details.

Details

By default, if ids is missing, the column GeneID of the slot geneAnno of each of the cellHTS objects in screens is taken for the annotation IDs when comparing the two data sets.

Value

A list with two components:

p.overlap	a vector giving the proportion of overlap in the screens' annotation.
isInBoth	a list of logical vectors, each of which with length equal to the product between nr. Well and nr. Plates in each screen, indicating whether the respective gene-perturbing reagent of that screen is also present in the other.

Author(s)

Ligia Braz [e-mail]

Examples

    ## Just for exemplification purposes, we consider the complete genome-wide screen "KcViab" 
    ## and its first 3 plates ("KcViabSmall"): 
    data(KcViab)
    data(KcViabSmall)
    screens <- list(KcViab, KcViabSmall)
    out <- screenMatch(screens)
    out$p.overlap
    sapply(out$isInBoth, sum)
    sapply(1:2, function(z) table(screens[[z]]$geneAnno$Plate[out$isInBoth[[z]]]))

cellHTS documentation built on Oct. 5, 2016, 4:40 a.m.