annotateFromBiomart: Annotate your Expression Set with biomaRt

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Annotate your Expression Set with biomaRt

Description

Annotate your Expression Set with biomaRt

Usage

annotateFromBiomart(
  obj,
  genes = featureNames(obj),
  filters = "ensembl_gene_id",
  attributes = c("ensembl_gene_id", "hgnc_symbol", "chromosome_name", "start_position",
    "end_position"),
  biomart = "ensembl",
  dataset = "hsapiens_gene_ensembl",
  ...
)

Arguments

obj	ExpressionSet object.
genes	Genes or rownames of the ExpressionSet.
filters	getBM filter value, see getBM help file.
attributes	getBM attributes value, see getBM help file.
biomart	BioMart database name you want to connect to. Possible database names can be retrieved with teh function listMarts.
dataset	Dataset you want to use. To see the different datasets available within a biomaRt you can e.g. do: mart = useMart('ensembl'), followed by listDatasets(mart).
...	Values for useMart, see useMart help file.

Value

ExpressionSet object with a fuller featureData.

Examples

u <- 'https://netzoo.s3.us-east-2.amazonaws.com/netZooR/unittest_datasets/'
bladder <- paste0(u, 'yarn/bladder.rdata')
skin <- paste0(u, 'yarn/skin.rdata')
download.file(bladder, destfile='netZooR/data/bladder.rdata')
download.file(skin, destfile='netZooR/data/skin.rdata')
data(skin)
# subsetting and changing column name just for a silly example
skin <- skin[1:10,]
colnames(fData(skin)) = paste("names",1:6)
biomart<-"ENSEMBL_MART_ENSEMBL";
genes <- sapply(strsplit(rownames(skin),split="\\."),function(i)i[1])
newskin <-annotateFromBiomart(skin,genes=genes,biomart=biomart)
head(fData(newskin)[,7:11])

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.