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

Description Usage Arguments Details Value Examples

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

1
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".

Details

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

Value

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

Examples

1
2
3
##	A toy example
##	example input files can be found at .libPaths()/sgRSEA/extdata.
##	sgCount('fqInfo.txt', 'library2.txt', 20, 'Test')

Example output



sgRSEA documentation built on May 2, 2019, 2:47 p.m.

Related to sgCount in sgRSEA...