sgRSEA (version 0.1)

sgCount: Generate a raw sgRNA read count table from fastq files

Description

Generate a raw sgRNA read count table from fastq files and an annotation file. The raw count table can be an input of UQnormalize() to apply sgRSEA(). Python is required.

Usage

sgCount(fqInfo, annotation, seqlen = 20, output_prefix = "sgCount")

Arguments

fqInfo

A tab-delimited text file. Rows represent fastq files and four cloumns are fastq filename, experimental condition name, starting and ending location of trimming of sgRNA reads. See the example below.

annotation

A tab-delimited annotation file. Columns are sgRNA name (1st), gene name (2nd), and sgRNA sequence read (3rd).

seqlen

Length of the sgRNA read.

output_prefix

A character() value. The name of output file is "output_prefix_count.txt".

Value

• Generate a tab-delimited file of sgRNA read count table. Columns are sgRNAs, genes and read counts at multiple experimental conditions.

Details

This function calls a python code located at system.file(package = "sgRSEA").

Examples

##	A toy example
##	example input files can be found at .libPaths()/sgRSEA/extdata.
##	sgCount('fqInfo.txt', 'library2.txt', 20, 'Test')