RNASeqEnvironmentSet: RNASeqEnvironmentSet

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

RNASeqEnvironmentSet

Description

Set up the environment for the following RNA-Seq workflow in R shell
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 background, please see RNASeqEnvironmentSet_CMD() function.

Usage

RNASeqEnvironmentSet(RNASeqRParam, which.trigger = "OUTSIDE",
  INSIDE.path.prefix = NA, install.hisat2 = TRUE,
  install.STAR = TRUE, install.stringtie = TRUE,
  install.gffcompare = TRUE, check.s4.print = TRUE)

Arguments

RNASeqRParam	S4 object instance of experiment-related parameters
which.trigger	Default value is OUTSIDE. User should not change this value.
INSIDE.path.prefix	Default value is NA. User should not change this value.
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.
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(RNASeqRParam = yeast)
## End(Not run)

HowardChao/RNASeqWorkflow documentation built on May 9, 2022, 10:49 a.m.