removeSharedOffTargets {scsR} | R Documentation

## removeSharedOffTargets

### Description

remove from an siRNA genome wide screen (screenA) all the oligos with a seed that is contained also in a second screen (screenB) in oligos designed to target the same genes (i.e. if an oligo X that target gene K in screenA is found to have the same seed as an oligo Y in screenB that targets gene K, then oligo X is removed from screenA). In this way we can remove from a screen all the oligos that have potentially the same type of off-targets as those in another screen. We suggest to perform thie step before running a benchmark on the shared hits (because we don't want the benchmark to count shared hits that are generated by possible shared off-target effects)

### Usage

    removeSharedOffTargets(screenA, screenB, seedColName="seed7",
                                          geneColName="GeneID",
                                          seqColName="siRNA_seq",
                                          removeGenes=FALSE)

### Arguments

`screenA` | screen to be filtered of the oligos that share the seed with oligos that target the same gene in a screenB
`screenB` | screenB
`seedColName` | name of the column that contains the seeds (character vector)
`geneColName` | name of the column that contains the gene identifiers (character vector)
`seqColName` | name of the column that contains the oligo sequences (character vector)
`removeGenes` | specify whether to remove just the oligos or the entire gene, as you would probably like to do when screenA is a pooled library (i.e. remove all the oligos that refer to a gene, even if only one oligos contains a seed that is common to oligos of screenB that refer to the same gene) (boolean)

### Value

return screenA filtered of the oligos that are similar in seed to those of screenB. (data frame)

### Author(s)

Andrea Franceschini

### Examples

    	data(uuk_screen)
    	data(uuk_screen_dh)

    	# reduce the size of the input datasets in order to make the example faster
    	# (you should not perform this operation in a real case)
    	uuk_screen=head(uuk_screen, n=2500)
    	uuk_screen_dh=head(uuk_screen_dh, n=2500)

    	uuk_qi = removeSharedOffTargets(add_seed(uuk_screen), add_seed(uuk_screen_dh))

[Package scsR version 1.16.0 Index]