systemdf: Wrapper of system calls in which input and output are all...

Description Usage Arguments Details Value Examples

View source: R/systemdf.R

Description

Wrapper of system calls in which input and output are all table-like files

Usage

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systemdf(cmd, envir = parent.frame(), verbose = FALSE)

Arguments

cmd

shell command

envir

environment where to look for variables encoded in cmd

verbose

whether print messages

Details

This function (system + data frame) provides a convinient way to invoke system calls in R. Since most of system calls expect tables as input and output, systemdf does following things step by step:

A simple example is as follows:

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    bed1 = circlize::generateRandomBed(nr = 1000)
    bed2 = circlize::generateRandomBed(nr = 1000)
    df = systemdf("bedtools closest -a `bed1` -b `bed2` | awk '$1==\"chr1\"'")  

Value

A data frame. If there is no line generated by the system call, the returned value is a three-column data frame with 0 row.

Examples

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# There is no example
NULL

jokergoo/cotools documentation built on May 18, 2017, 6:05 a.m.