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

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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

none

Author(s)

Jan Winter

Examples

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#check.caRpools()

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