ccr.getLibrary: Convert library inputs in a standard library annotaion.

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

Convert library inputs in a standard library annotaion.

Description

This function takes as input a string identifying one of the sgRNA built-in library or a file name (comprehensive of the full path) to create a data frame with the standard format of the annotaion library requested by CRISPRcleanR. This is a utility function that runs automatically as part of the ccr.AnalysisPipeline.

Usage

  ccr.getLibrary(
    library_builtin,
    library_file,
    verbose = FALSE
  ) 

Arguments

library_builtin	A string containing the name of one of the libraries whose annotation is available in CRISPRcleanR.
library_file	A string specifying the path to a file containing the sgRNA annotations in TXT / TSV format, with columns for sgRNA ID ("CODE"), targeted genes ("GENES"), genomic coordinates, and possibly other information. This should be formatted as the KY_Library_v1.0 data object containing the annotation of the sgRNA library presented in [1]. If FASTQ files are used as input the annotation must include also a column "seq" with the nucleotidic sequence of the sgRNAs. This argument is ignored if a built-in library is specified.
verbose	Technical parameter undocumented. Used for the integration in web architecture.

Value

A data frame compliant with the annotation library format requested by CRIPRcleanR.

Author(s)

Paolo Cremaschi ([e-mail])

See Also

ccr.AnalysisPipeline

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