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Last data update: 2014.03.03

R: Test caRpools installation and dependent software

check.caRpools

R Documentation

Test caRpools installation and dependent software

Description

You can verify that the MIACCS.xls file as well as the used template file and all necessary scripts are found by calling 'check.caRpools()'. CaRpools also uses MAGeCK to look for enriched or depleted genes within your screening data. Please note that MAGeCK needs to be installed correctly, this can be tested by 'check.caRpools'.

Usage

check.caRpools(packages=TRUE, files=TRUE, mageck=TRUE, bowtie2=TRUE,
pandoc=TRUE, skip.updates=TRUE, template=NULL, scripts=TRUE, miaccs="MIACCS.xls")

Arguments

`packages`	if TRUE, packages will be checked using load.packages()
`files`	If TRUE, MIACCS as well as data and scripts folder will be checked in addition to CRISPR-mapping.pl and CRISPR-extract.pl.
`mageck`	If TRUE, mageck installation is checked.
`bowtie2`	if TRUE, bowtie2 installation is checked.
`pandoc`	if TRUE, pandoc installation is checked.
`skip.updates`	if TRUE, updates are skipped during package check.
`template`	Rmd template file name to use.
`scripts`	if TRUE, checks for perl scripts CRISPR-mapping and CRISPR-extract.pl.
`miaccs`	Filename of MIACCS file. Will be checked for proper loading.

Details

none

Value

This function does not return any value.

Note