RNASeqGoKegg: RNASeqGoKegg

Description Usage Arguments Value Author(s) Examples

View source: R/cmd_batch_rnaseq_GO_KEGG.R

Description

Run Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis in R shell.
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 background, please see RNASeqGoKegg_CMD() function.

Usage

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RNASeqGoKegg(RNASeqRParam, which.trigger = "OUTSIDE",
  INSIDE.path.prefix = NA, OrgDb.species, go.level = 3, input.TYPE.ID,
  KEGG.organism, 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.

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 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

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data(yeast)
## Not run: 
RNASeqGoKegg(RNASeqRParam  = yeast,
             OrgDb.species = "org.Sc.sgd.db",
             go.level = 3,
             input.TYPE.ID = "GENENAME",
             KEGG.organism = "sce")
## End(Not run)

HowardChao/RNASeqR documentation built on Sept. 6, 2019, 8:52 a.m.