int_file_import: Integration site file import and summary statistics

In gbedwell/rigrag: Identification of Recurrently Targeted Genes and Recurrently Avoided Genes During HIV-1 Infection

Description

Imports integration site files. Calculates the number of genic integration sites and the fraction of genic integration events per sample. Calculates gene length per gene.

Usage

int_file_import(files, sample.ids, collapsed = c(TRUE, FALSE))

Arguments

files	List of integration site files containing the data to be analyzed. Generated with generate_file_list()
sample.ids	List of sample identifiers for each file in the file list. Defined with list(). The order of the sample identifiers must match the order of the files listed in the file list. Spaces and special characters like '+' and '#' are OK in the sample identifiers. Files written within package functions named using sample identifiers will have their names cleaned to remove spaces and select special characters.
collapsed	If "TRUE", the number of occurrences of each gene per sample are counted and the collapsed data is returned. If "FALSE", every integration event into every gene is returned.

Examples

int_file_import()

gbedwell/rigrag documentation built on June 23, 2021, 10:32 p.m.