ccr.logFCs2chromPos: Genomic sorting of sgRNAs' log fold changes.

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

Genomic sorting of sgRNAs' log fold changes.

Description

This function maps genome-wide sgRNAs' log fold changes (averaged across replicates) on the genome and returns them sorted according to the position of their targeted region on the chromosomes.

Usage

ccr.logFCs2chromPos(foldchanges, libraryAnnotation)

Arguments

foldchanges

A data frame containing genome-wide sgRNAs' log fold changes, one column per library transfection replicate, with first and second column containing the sgRNAs' identifiers and the HGNC symbols of the targeted genes, respectively. This can be generated from raw count files using the ccr.NormfoldChanges function.

libraryAnnotation

A data frame containing the sgRNAs' genome-wide annotations with at least a named row for each of the sgRNAs included in the foldchanges data frame provided in input. The following columns/headers should be present in this data frame (additional columns will be ignored): GENES: string vector containing the HGNC symbols of the genes targeted by the sgRNA under consideration; EXONE: string vector containing the gene exon targeted by the sgRNA under consideration (these should include the prefix "ex" followed by the exone number); CHRM: string vector the chromosome of the gene targeted by the sgRNA under consideration (X and Y chromosome should be specified as "X" and "Y"); STRAND: string vector containing the strand targeted by the sgRNA under consideration ("+" or "-"); STARTpop: numeric vector containing the genomic coordinate of the starting position of the region targeted by the sgRNA under consideration; ENDpos: numeric vector containing the genomic coordinate of the ending position of the region targeted by the sgRNA under consideration; Additiol columns can be optionally included and will be ignored by this function. The annation for the genome-wide sgRNA library presented in [1] is included in the KY_Library_v1.0 data object, formatted as described above.

Value

A data frame with a named row per each sgRNA and the following columns/headers:

• CHR: the chromosome where the gene targeted by the sgRNA under consideration resides;

• startp: the genomic coordinate of the starting position of the region targeted by the sgRNA under consideration;

• endp: the genomic coordinate of the ending position of the region targeted by the sgRNA under consideration;

• avgFC: the log fold change of the sgRNA averaged across replicates;

• BP: the genomic coordinate of the sgRNA defined as STARTpos+(ENDpos-STARTpos)/2.

Author(s)

Francesco Iorio ([e-mail])

References

[1] Tzelepis K, Koike-Yusa H, De Braekeleer E, Li Y, Metzakopian E, Dovey OM, Mupo A, Grinkevich V, Li M, Mazan M, Gozdecka M, Onishi S, Cooper J, Patel M, McKerrell T, Chen B, Domingues AF, Gallipoli P, Teichmann S, Ponstingl H, McDermott U, Saez-Rodriguez J, Huntly BJP, Iorio F, Pina C, Vassiliou GS, Yusa K. A CRISPR dropout screen identifies genetic vulnerabilities and therapeutic targets in acute myeloid leukaemia. Cell Reports 2016 Oct 18;17(4):1193-1205

See Also

ccr.NormfoldChanges, KY_Library_v1.0

Examples

## Not run: 
    data(KY_Library_v1.0)
    fn<-paste(system.file('extdata', package = 'CRISPRcleanR'),'/A2058_counts.tsv',sep='')
    normANDfcs<-ccr.NormfoldChanges(fn,min_reads=30,
                                    EXPname='Example',
                                    libraryAnnotation=KY_Library_v1.0)
    mappedLogFCs<-ccr.logFCs2chromPos(normANDfcs$logFCs,KY_Library_v1.0)
    head(mappedLogFCs)

## End(Not run)

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