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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