EMA (version 1.4.5)

bioMartAnnot: Annotation of probesets using biomaRt

Description

Annot input IDs using the biomaRt package.

Usage

bioMartAnnot(data, inputTypeId, outputTypeId =c("entrezgene","hgnc_symbol",
"ensembl_gene_id", "description", "chromosome_name", "start_position",
"end_position", "band", "strand") , dataset= c("hsapiens_gene_ensembl"),
database = "ensembl",  sort.by = NULL, outfile = NA)

Arguments

data

A data.frame with the input names as rownames or a vector of probesets

inputTypeId

Input Ids type. see details

outputTypeId

Output Ids type. if NULL the description of some genes names are returned. see details

dataset

The dataset used for the annotation

database

The database used for the annotation

sort.by

optional. Allow to sort the output data.frame

outfile

optional. Write an html file with the results

Details

This function is based on the biomaRt package. First, you have to define the database and the dataset you want to use for the annotation (default dataset= c("hsapiens_gene_ensembl"), database = "ensembl"). The input IDs type have to be defined as in the biomaRt package. The listFilters() functions of the biomaRt package lists the available input type. If the inputs are probe names, use the microarray name : affy_hg_u95a,affy_hg_u95av2,affy_hg_u133a_2,affy_hg_u133a, affy_hg_u133b,affy_hg_u133_plus_2, illumina_humanwg_6_v2, ... Use the biomaRt function 'listAttributes()', to select your output. By default, the function returns "description", "chromosome_name", "start_position", "end_position", "band", "strand", and "ensembl_gene_id".

See Also

useMart

Examples

# NOT RUN {
## load data
data(marty)

##Annotations example
bioMartAnnot(rownames(marty)[1:50], inputTypeId ="affy_hg_u133_plus_2",
   outputTypeId =c("entrezgene","hgnc_symbol"),
   dataset=c("hsapiens_gene_ensembl"),database = "ensembl")
# }