removeSharedOffTargets: removeSharedOffTargets

In scsR: SiRNA correction for seed mediated off-target effect

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))

scsR documentation built on April 28, 2020, 7:11 p.m.