All_Steps_Interface_CMD: All_Steps_Interface_CMD

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

All_Steps_Interface_CMD

Description

A functios to run all the steps with in one function. This function execute in the background:

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

All_Steps_Interface_CMD(RNASeqRParam, RNASeqQualityAssessment.RUN = TRUE,
  RNASeqReadProcess.RUN = TRUE, RNASeqDifferentialAnalysis.RUN = TRUE,
  RNASeqGoKegg.RUN = TRUE, OrgDb.species, go.level = 3, input.TYPE.ID,
  KEGG.organism, run = TRUE, check.s4.print = TRUE)

Arguments

RNASeqRParam	S4 object instance of experiment-related parameters
RNASeqQualityAssessment.RUN	Default value is TRUE. Set FALSE to skip "Quality Assessment" step.
RNASeqReadProcess.RUN	Default value is TRUE. Set FALSE to skip "RNASeq Read Process" step.
RNASeqDifferentialAnalysis.RUN	Default value is TRUE. Set FALSE to skip "RNASeq Differential Analysis" step.
RNASeqGoKegg.RUN	Default value is TRUE. Set FALSE to skip "RNASeq Go & Kegg" step.
OrgDb.species	the genome wide annotation packages of species on Bioconductor. Currently, there are 19 supported genome wide annotation packages of species.
go.level	the depth of acyclic graph in GO analysis
input.TYPE.ID	The gene name type in OrgDb.species annotation packahge.
KEGG.organism	the species that are supported for KEGG analysis. Currently, there are more than 5000 supported species genome. Check the valid species terms on https://www.genome.jp/kegg/catalog/org_list.html
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)

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