memcrispr.count: Count occurrences of each guide in aligned data.

In grimbough/MEMcrispR: Mixed Effects Model for the analysis of CRISPR screens

Description

This function expects to be provided a folder containing BAM files produced either by memcrispr.align or another aligner. It will count the number of reads mapping to each guide in the reference and produce a table of the same structure as produced by samtools idxstat.

Usage

memcrispr.count(
  path,
  sampleSheet = NULL,
  outputDir = NULL,
  guideLibraries = c("GeCKOv2_A", "GeCKOv2_B"),
  ncores = 4
)

Arguments

path	Full file path to the folder containing the data.
sampleSheet	Name of the file specifying the structure of the experiment. If left NULL a default of 'SampleSheet.txt' is used.
outputDir	Full path to the location where output files should be written. If left NULL the current working directory is used.
guideLibraries	Names of libraries to align against. These can be paths to files for custom libraries not included in the package.
ncores	The number of CPU cores to be used by the Rsubread aligner. Defaults to 4.

grimbough/MEMcrispR documentation built on Feb. 4, 2021, 5:26 a.m.