[R] Unable to extract gene list from chromosome

[pooja sinha]

Hi David,

Sorry I forgot to attach the file. Now it's attached.


Thanks,
Puja

On Thu, Apr 8, 2021 at 6:01 PM David Winsemius <dwinsemius using comcast.net>
wrote:

>
> 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
> >
> >       [[alternative HTML version deleted]]
> >
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