Mohammad Tanvir Ahamed
2013-Feb-08 06:07 UTC
[R] Conflict command getSequence {biomaRt} and getSequence {seqinr} !!
Hi ! Facing problem with " getSequence" commend . when only biomaRt package loaded the following example working well>mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart)show(seq) but when i have loaded the seqinr, i got problem with same commend .> mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") > seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart)Error in length(x) : 'x' is missing I need to use biomaRt and seqinr package together as i will use other commends from biomaRt and seqinr package . Thanks . /.......Tanvir Ahamed [[alternative HTML version deleted]]
Pascal Oettli
2013-Feb-08 06:14 UTC
[R] Conflict command getSequence {biomaRt} and getSequence {seqinr} !!
Hi, You can write "biomaRt::getSequence" instead of "getSequence". Hope this helps, Pascal Le 08/02/2013 15:07, Mohammad Tanvir Ahamed a ?crit :> Hi ! > > Facing problem with " getSequence" commend . > when only biomaRt package loaded the following example working well > > >> mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >> seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) > > show(seq) > > but when i have loaded the seqinr, i got problem with same commend . > >> mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >> seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) > Error in length(x) : 'x' is missing > > I need to use biomaRt and seqinr package together as i will use other commends from biomaRt and seqinr package . > > Thanks . > > > > /.......Tanvir Ahamed > > [[alternative HTML version deleted]] > > > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >