mock_missing_FGC_data: mock_missing_FGC_data

In alex-kalinka-cruk/fgcQC: QC metric calculations for CRISPR screen data produced at the FGC

Description

Function to write out mock data that is missing from the inputs to 'QC_fgc_crispr_data'. The mock data is written to temporary files that are deleted when the 'R' session ends.

Usage

mock_missing_FGC_data(analysis_config, combined_counts, bcl2fastq, library)

Arguments

analysis_config	A path to a valid analysis config JSON file to be used as input for the AZ-CRUK CRISPR analysis pipeline.
combined_counts	A path to a valid combined counts csv file (produced by the AZ-CRUK CRISPR analysis pipeline).
bcl2fastq	A character string giving one or more paths to valid 'bcl2fastq2' summary output JSON files (paths separated by commas). 'NULL' if missing.
library	A valid path to a library tsv file in which the first column gives the sgRNA sequence and the second column gives the sgRNA ID (produced by the AZ-CRUK CRISPR reference data generation pipeline). 'NULL' if missing.

Value

A named list of temporary file names pointing to mocked data.

alex-kalinka-cruk/fgcQC documentation built on June 23, 2020, 9:05 p.m.