[R] Unable to extract gene list from chromosome

[David Winsemius]

On 4/8/21 2:30 PM, pooja sinha wrote:
> Hi All,
>
> I am trying to extract gene list from chromosome number and position, for
> that I am using biomaRt in R but I am getting error messages as shown
> below. Also below is the code I am using for extraction.
>
> library("biomaRt")
> listMarts()
> ensembl <- useMart("ensembl")
> datasets <- listDatasets(ensembl)
> ensembl = useDataset("rnorvegicus_gene_ensembl",mart=ensembl)
> AT_AC_Gene <- read.csv("AT-AC-methylkit_biomart-4-7-21.csv",header=T)


#--- a this point I get

Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
   cannot open file 'AT-AC-methylkit_biomart-4-7-21.csv': No such file 
or directory

> attributes <-
> c("external_gene_name","ensembl_gene_id","start_position","end_position","rgd_symbol","chromosome_name")
> filters <- c("chromosome_name","start","end")
> values <- list(AT_AC_Gene$chr,AT_AC_Gene$start,AT_AC_Gene$end)
> final_1 <- getBM(attributes=attributes, filters=filters, values=values,
> mart=ensembl)
>
> The code runs well without any error but the final1 output has 0
> observations of 6 variables. Why?
>
> Can anyone help me with this?


You are more likely to get a useful response on the BioC mailing list. 
It appears you have a dependenciy of a csv file that you have not told 
us about.


-- 

David

>
>
> Thanks,
>
> Puja
>
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>
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