| bioMartAnnot {EMA} | R Documentation |
Annot input IDs using the biomaRt package.
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)
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 |
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".
EMA group
## 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")
## End(Not run)