ccr.geneMeanFCs: Gene level log fold changes

In francescojm/CRISPRcleanR: Unsupervised correction of gene independent cell responses to CRISPR-cas9 targeting

Gene level log fold changes

Description

This functions computes gene level log fold changes based on average log fold changes of targeting sgRNAs

Usage

ccr.geneMeanFCs(sgRNA_FCprofile, libraryAnnotation)

Arguments

sgRNA_FCprofile	A named numerical vector containing the sgRNAs' log fold-changes, with names corresponding to sgRNAs identifiers.
libraryAnnotation	A data frame containing the sgRNA library annotation (with same format of KY_Library_v1.0).

Value

A numerical vector containing gene average log fold-changes, with corresponding HGNC symbols as names.

Author(s)

Francesco Iorio ([e-mail])

See Also

KY_Library_v1.0

Examples

## loading corrected sgRNAs log fold-changes and segment annotations for
## an example cell line (EPLC-272H)
data(EPLC.272HcorrectedFCs)


## loading sgRNA library annotation
data(KY_Library_v1.0)

## storing sgRNA log fold-changes in a named vector
FCs<-EPLC.272HcorrectedFCs$corrected_logFCs$avgFC
names(FCs)<-rownames(EPLC.272HcorrectedFCs$corrected_logFCs)

## computing gene level log fold-changes
geneFCs<-ccr.geneMeanFCs(FCs,KY_Library_v1.0)

head(geneFCs)

francescojm/CRISPRcleanR documentation built on April 30, 2023, 5:41 a.m.