Container for storing mappings of genes to annotation categories
such as gene ontologies (GO), pathways or conserved sequence domains.
The catmap slot stores a list of data.frames providing the direct
assignments of genes to annotation categories (e.g. gene-to-GO mappings);
catlist is a list of lists of all direct and indirect associations to
the annotation categories (e.g. genes mapped to a pathway); and idconv
allows to store a lookup-table for converting identifiers (e.g. array feature
ids to gene ids).
Objects from the Class
Objects can be created by calls of the form new("catDB", ...).
Slots
catmap:
Object of class "list"list of data.frames
catlist:
Object of class "list"list of lists
idconv:
Object of class "ANY"list of data.frames
Methods
catlist
signature(x = "catDB"): extracts data from catlist slot
catmap
signature(x = "catDB"): extracts data from catmap slot
coerce
signature(from = "list", to = "catDB"): as(list, "catDB")
idconv
signature(x = "catDB"): extracts data from idconv slot
names
signature(x = "catDB"): extracts slot names
show
signature(object = "catDB"): summary view of catDB objects
showClass("catDB")
## Not run:
## Obtain annotations from BioMart
listMarts() # To choose BioMart database
m <- useMart("ENSEMBL_MART_PLANT"); listDatasets(m)
m <- useMart("ENSEMBL_MART_PLANT", dataset="athaliana_eg_gene")
listAttributes(m) # Choose data types you want to download
go <- getBM(attributes=c("go_accession", "tair_locus", "go_namespace_1003"), mart=m)
go <- go[go[,3]!="",]; go[,3] <- as.character(go[,3])
write.table(go, "GOannotationsBiomart_mod.txt", quote=FALSE, row.names=FALSE, col.names=FALSE, sep="\t")
## Create catDB instance (takes a while but needs to be done only once)
catdb <- makeCATdb(myfile="GOannotationsBiomart_mod.txt", lib=NULL, org="", colno=c(1,2,3), idconv=NULL)
catdb
## End(Not run)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(systemPipeR)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: ShortRead
Loading required package: BiocParallel
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/systemPipeR/catDB-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: catDB-class
> ### Title: Class '"catDB"'
> ### Aliases: catDB-class catlist,catDB-method catmap,catDB-method
> ### coerce,list,catDB-method idconv,catDB-method names,catDB-method
> ### show,catDB-method
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("catDB")
Class "catDB" [package "systemPipeR"]
Slots:
Name: catmap catlist idconv
Class: list list ANY
> ## Not run:
> ##D ## Obtain annotations from BioMart
> ##D listMarts() # To choose BioMart database
> ##D m <- useMart("ENSEMBL_MART_PLANT"); listDatasets(m)
> ##D m <- useMart("ENSEMBL_MART_PLANT", dataset="athaliana_eg_gene")
> ##D listAttributes(m) # Choose data types you want to download
> ##D go <- getBM(attributes=c("go_accession", "tair_locus", "go_namespace_1003"), mart=m)
> ##D go <- go[go[,3]!="",]; go[,3] <- as.character(go[,3])
> ##D write.table(go, "GOannotationsBiomart_mod.txt", quote=FALSE, row.names=FALSE, col.names=FALSE, sep="\t")
> ##D
> ##D ## Create catDB instance (takes a while but needs to be done only once)
> ##D catdb <- makeCATdb(myfile="GOannotationsBiomart_mod.txt", lib=NULL, org="", colno=c(1,2,3), idconv=NULL)
> ##D catdb
> ## End(Not run)
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.