RNASeqGoKegg_CMD: RNASeqGoKegg_CMD

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

RNASeqGoKegg_CMD

Description

Run Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis in background.
This function do Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis :

1. Gene Ontology(GO) :
   

   1. Do GO function classification analysis.
      

   2. Do GO function enrichment analysis.
      

   3. Visualization : bar plot, dot plot etc.
      

2. Kyoto Encyclopedia of Genes and Genomes(KEGG) :
   

   1. Do KEGG pathway enrichment analysis
      

   2. Pathway visulization with pathview package. KEGG webpage pathway url will also be created
      

If you want to do GO functional analysis and KEGG pathway analysis for the following RNA-Seq workflow in R shell, please see RNASeqGoKegg() function.

Usage

RNASeqGoKegg_CMD(RNASeqRParam, 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
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: 
RNASeqGoKegg_CMD(RNASeqRParam  = yeast,
                 OrgDb.species = "org.Sc.sgd.db",
                 go.level = 3,
                 input.TYPE.ID = "GENENAME",
                 KEGG.organism = "sce")

## End(Not run)

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