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

In jokergoo/cotools: R functions

Description

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

Usage

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:

• use backtick to mark variables which are data frames or other variables which can be converted to data frames by as.data.frame

• extract data frames

• write data frames into temporary files

• replace variables names with paths that correspond to temporary files

• make the system call

• finally send back the output by piping back to R

A simple example is as follows:

    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

# There is no example
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jokergoo/cotools documentation built on May 19, 2019, 6:24 p.m.