ccr.VisDepAndSig: Depletion profile visualisation with genes signatures...

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

Depletion profile visualisation with genes signatures superimposed and recall

Description

This functions ranks the gene (or sgRNAs) log fold changes. Based on this it determines a log fold change threshold based on a user defined false discovery rate when classifying two gene (sgRNA) positive/negative references sets (tipically core-fitness-essential and non-essential genes), and it computes the Recall (or True Positive Rate) of genes in other user defined sets at the determined threshold. It produces a plot where the log fold changes are visualised alongside the rank positions of the genes included in the inputted sets and, their recall and the determined FDR threshold.

Usage

ccr.VisDepAndSig(FCsprofile,SIGNATURES,TITLE='',
                 pIs=NULL,nIs=NULL,
                 th=0.05,plotFCprofile=TRUE)

Arguments

FCsprofile	A numerical vector containing gene average depletion log fold changes (or sgRNAs' depletion log fold changes) with names corresponding to HGNC symbols (or sgRNAs' identifiers).
SIGNATURES	A named list of vectors containing HGNC gene symbols. Two of these lists are used as classification template (respectively for positive and negative cases) to determine a log fold-change threshold providing a user defined classification false discovery rate.
TITLE	A string specifiying the title of the plot.
pIs	The index position of the signature that contains the positive cases of the classification template.
nIs	The index position of the signature that contains the negative cases of the classification template.
th	A numerical value specifying the desired classification false discovery rate (this must be a real number between 0 and 1).
plotFCprofile	A logic value specifying whether the log fold changes should be plotted.

Value

A named numerical vector containing recall scores for all the inputted signatures at the computed false discovery rate threshold for log fold-changes.

Author(s)

Francesco Iorio ([e-mail])

See Also

ccr.ROC_Curve, ccr.PrRc_Curve

Examples

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

## loading reference sets of essential and non-essential genes
data(BAGEL_essential)
data(BAGEL_nonEssential)

## loading other sets of core fitness genes
data(EssGenes.ribosomalProteins)
data(EssGenes.DNA_REPLICATION_cons)
data(EssGenes.KEGG_rna_polymerase)
data(EssGenes.PROTEASOME_cons)
data(EssGenes.SPLICEOSOME_cons)

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

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

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


## Assembling a named list with all the considered gene sets
SIGNATURES<-list(Ribosomal_Proteins=EssGenes.ribosomalProteins,
                 DNA_Replication = EssGenes.DNA_REPLICATION_cons,
                 RNA_polymerase = EssGenes.KEGG_rna_polymerase,
                 Proteasome = EssGenes.PROTEASOME_cons,
                 Spliceosome = EssGenes.SPLICEOSOME_cons,
                 CFE=BAGEL_essential,
                 non_essential=BAGEL_nonEssential)

## Visualising log fold change profile with superimposed signatures specifying
## that the reference gene sets are in positions 6 and 7
Recall_scores<-ccr.VisDepAndSig(FCsprofile = FCs,
                            SIGNATURES = SIGNATURES,
                            TITLE = 'EPLC-272H',
                            pIs = 6,
                            nIs = 7)

Recall_scores

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