View source: R/all_steps_interface.R
All_Steps_Interface | R Documentation |
Set up the environment for the following RNA-Seq workflow in R shell
This function do 4 things :
Create file directories.
Install necessary tools.
Export 'RNASeq_bin/' to the R environment.
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.
All_Steps_Interface(RNASeqRParam, which.trigger = "OUTSIDE", INSIDE.path.prefix = NA, RNASeqQualityAssessment.RUN = TRUE, RNASeqReadProcess.RUN = TRUE, RNASeqDifferentialAnalysis.RUN = TRUE, RNASeqGoKegg.RUN = TRUE, OrgDb.species, go.level = 3, input.TYPE.ID, KEGG.organism, check.s4.print = TRUE)
RNASeqRParam |
S4 object instance of experiment-related parameters |
which.trigger |
Default value is |
INSIDE.path.prefix |
Default value is |
RNASeqQualityAssessment.RUN |
Default value is |
RNASeqReadProcess.RUN |
Default value is |
RNASeqDifferentialAnalysis.RUN |
Default value is |
RNASeqGoKegg.RUN |
Default value is |
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 |
check.s4.print |
Default |
None
Kuan-Hao Chao
data(yeast) ## Not run: RNASeqEnvironmentSet(RNASeqRParam = yeast) ## End(Not run)
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