ccr.PlainTsvFile: Saving a sgRNA counts' object in plain tsv file

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

Saving a sgRNA counts' object in plain tsv file

Description

This function takes in input a sgRNA counts' object, as outputted (for example) by the ccr.NormfoldChanges function and saves it as plaing tab delimited text file (which can be processed by MAGeCK [1]).

Usage

ccr.PlainTsvFile(sgRNA_count_object,
                 fprefix = "",
                 path = "./")

Arguments

sgRNA_count_object	sgRNA counts data object.
fprefix	A string specifying a name prefix of the tsv file which will contain the inputted sgRNA counts data object.
path	A string specifying the location where the tsv file will be saved.

Value

A string specifying the complete path of the saves tsv file.

Author(s)

Francesco Iorio ([e-mail])

References

[1] Li, W., Xu, H., Xiao, T., Cong, L., Love, M. I., Zhang, F., et al. (2014). MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biology, 15(12), 554. [2] Hart, T., & Moffat, J. (2016). BAGEL: a computational framework for identifying essential genes from pooled library screens. BMC Bioinformatics, 17(1), 164.

See Also

ccr.NormfoldChanges

Examples

## Not run: 
## Loading sgRNA library annotation file
data(KY_Library_v1.0)

## Deriving the path of the file with the example dataset,
## from the mutagenesis of the EPLC-272H colorectal cancer cell line
fn<-paste(system.file('extdata', package = 'CRISPRcleanR'),
          '/EPLC-272H_counts.tsv',sep='')

## Loading, median-normalizing and computing fold-changes for the example dataset
normANDfcs<-ccr.NormfoldChanges(fn,min_reads=30,
                                EXPname='EPLC-272H',
                                libraryAnnotation = KY_Library_v1.0,
                                display=FALSE)
                                
## saving median-normalised sgRNA counts' as a plain tsv file in ./EPLC-272H_sgRNA_count.tsv
uncorrected_fn<-ccr.PlainTsvFile(sgRNA_count_object = normANDfcs$norm_counts,fprefix = 'EPLC-272H')

uncorrected_fn

## End(Not run)

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