Entering edit mode
3.8 years ago
mintdrink
•
0
Hey! This is a follow-up question to one where I asked for help coding (in R) a way to convert gene accession numbers to gene names. Here is my code, where charg
is a character vector of the gene accession ID's of the data set resdata
:
charg <- resdata$genes
head(charg)
ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
theBM <- getBM(attributes='ensembl_gene_id','hgnc_symbol',
filters = 'external_gene_name',
values = charg,
mart = ensembl)
resdata <- merge.data.frame(resdata, theBM, by.x="genes",by.y="ensembl_gene_id")
Here's some output (where I'm struggling):
> head(charg)
[1] "ENSG00000261150.2" "ENSG00000164877.18" "ENSG00000120334.15"
[4] "ENSG00000100906.10" "ENSG00000182759.3" "ENSG00000124145.6"
> dim(theBM)
[1] 0 1
> head(theBM)
[1] ensembl_gene_id
<0 rows> (or 0-length row.names)
> dim(resdata)
[1] 20381 11
> resdata <- merge.data.frame(resdata, theBM, by.x="genes",by.y="ensembl_gene_id")
> dim(resdata) #after merge
[1] 0 11 #isn't correct -- just row names! where'd my genes go?
Thank you.