gson_KEGG_mapper: Build KEGG annotation for novel species using KEGG Mapper

In GuangchuangYu/clusterProfiler: A universal enrichment tool for interpreting omics data

Build KEGG annotation for novel species using KEGG Mapper

Description

KEGG Mapper service can annotate protein sequences for novel species with KO database, and KO annotation need to be converted into Pathway or Module annotation, which can then be used in 'clusterProfiler'

Usage

gson_KEGG_mapper(
  file,
  format = c("BLAST", "Ghost", "Kofam"),
  type = c("pathway", "module"),
  species = NULL,
  ...
)

Arguments

file	the name of the file which comes from the KEGG Mapper service, see Details for file format
format	string indicate format of KEGG Mapper result
type	string indicate annotation database
species	your species, NULL if ignored
...	pass to gson::gson()

Details

File is a two-column dataset with K numbers in the second column, optionally preceded by the user's identifiers in the first column. This is consistent with the output files of automatic annotation servers, BlastKOALA, GhostKOALA, and KofamKOALA. KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data by BLAST and GHOSTX searches, respectively, against a nonredundant set of KEGG GENES. KofamKOALA is a new member of the KOALA family available at GenomeNet using the HMM profile search, rather than the sequence similarity search, for K number assignment. see https://www.kegg.jp/blastkoala/, https://www.kegg.jp/ghostkoala/ and https://www.genome.jp/tools/kofamkoala/ for more information.

Value

a gson instance

Examples

## Not run: 
 file = system.file('extdata', "kegg_mapper_blast.txt", package='clusterProfiler')
 gson_KEGG_mapper(file, format = "BLAST", type = "pathway")

## End(Not run)

GuangchuangYu/clusterProfiler documentation built on Nov. 15, 2024, 3:05 p.m.