cleanBM {biomaRt}R Documentation

Clear getBM result from duplicates

Description

This function removes duplicated results retrieved by getBM. Two sets of IDs are required in the query result to be able to use this function. The query id that was used in the getBM function as filter and was also used as attribute to retrieve e.g. affy_hg_u95av2 and a result id e.g. GO identifiers that were retrieved.

Usage

cleanBM(bmresult, query_id_col=1, result_id_col=2)

Arguments

bmresult A data.frame that was returned by the getBM function
query_id_col Index of column of the query id in the result
result_id_col Index of column of the result id in the result

Author(s)

Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck

Examples

if(interactive()){
mart <- useMart("ensembl")
datasets <- listDatasets(mart)
mart<-useDataset("hsapiens_gene_ensembl",mart)
bm=getBM(attributes=c("affy_hg_u95av2","go","hgnc_symbol","chromosome_name","band"),filters="affy_hg_u95av2",values=c("1939_at","1000_at","1454_at"), mart=mart)

writeLines("## before duplicate removal ##")

print(bm)

writeLines("## After duplicate removal ##")
print(cleanBM(bm,1,2))
}

[Package biomaRt version 1.8.2 Index]