RNASeqEnvironmentSet_CMD: RNASeqEnvironmentSet_CMD

In Kuanhao-Chao/RNASeqR: RNASeqR: an R package for automated two-group RNA-Seq analysis workflow

RNASeqEnvironmentSet_CMD

Description

Set up the environment for the following RNA-Seq workflow in background.
This function do 4 things :

1. Create file directories.
   

2. Install necessary tools.
   

3. Export 'RNASeq_bin/' to the R environment.
   

4. Check command of tools.
   

First it will create 'gene_data/', 'RNASeq_bin/', 'RNASeq_results/', 'Rscript/', 'Rscript_out/' directories.
Afterwards, 'Hisat2', 'Stringtie', 'Gffcompare' will be installed under 'RNASeq_bin/Download/' and be unpacked under 'RNASeq_bin/Unpacked/'.
'RNASeq_bin/' will be added to the R environment and validity of tools will be checked.
Any ERROR occurs will be reported and the program will be terminated.
If you want to set up the environment for the following RNA-Seq workflow in R shell, please see RNASeqEnvironmentSet() function.

Usage

RNASeqEnvironmentSet_CMD(RNASeqRParam, install.hisat2 = TRUE,
  install.STAR = TRUE, install.stringtie = TRUE,
  install.gffcompare = TRUE, run = TRUE, check.s4.print = TRUE)

Arguments

RNASeqRParam	S4 object instance of experiment-related parameters
install.hisat2	Whether to install 'HISAT2' in this function step. Default value isTRUE. Set FALSE to skip 'HISAT2' installation.
install.STAR	Whether to install 'STAR' in this function step. Default value isTRUE. Set FALSE to skip 'STAR' installation.
install.stringtie	Whether to install 'StringTie' in this function step. Default value is TRUE. SetFALSE to skip 'StringTie' installation.
install.gffcompare	Whether to install 'Gffcompare' in this function step. Default value is TRUE. SetFALSE to skip 'Gffcompare' installation.
run	Default value is TRUE. If TRUE, 'Rscript/Environment_Set.R' will be created and executed. The output log will be stored in 'Rscript_out/Environment_Set.Rout'. If False, 'Rscript/Environment_Set.R' will be created without executed.
check.s4.print	Default TRUE. If TRUE, the result of checking RNASeqRParam will be reported in 'Rscript_out/Environment_Set.Rout'. If FALSE, the result of checking RNASeqRParam will not be in 'Rscript_out/Environment_Set.Rout'.

Value

None

Author(s)

Kuan-Hao Chao

Examples

data(yeast)
## Not run: 
RNASeqEnvironmentSet_CMD(yeast)
## End(Not run)

Kuanhao-Chao/RNASeqR documentation built on May 12, 2022, 8:15 a.m.