screenMatch {cellHTS} | R Documentation

## Matching the gene annotation of two 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 ligia@ebi.ac.uk

### 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]]]))

[Package cellHTS version 1.10.0 Index]