Hi,

I am trying to convert "chromosome postions" to "hgnc_symbol" using R. I referred the below site. http://statisticalrecipes.blogspot.com/2012/08/biomart-find-gene-name-using-chromosome.html

The code is below.

Load the library

library(biomaRt)

Define biomart object

mart <- useMart(biomart="ensembl", dataset="hsapiensgeneensembl")

Gives a list of all possible annotations; Currently there are 1668 listed

listAttributes(mart)

I chose to filter by: chromosome_name, start, end

listFilters(mart)

Read in tab-delimited file with three columns: chromosome number, start position and end position

positions <- read.table("positions.txt")

Extract HGNC gene symbol

results <- getBM(attributes = c("hgncsymbol", "chromosomename", "startposition", "endposition"), filters = c("chromosome_name", "start", "end"), values = list(positions[,1], positions[,2], positions[,3]), mart = mart)

================================================================================ After I got to run the code, I got this error message

*"Error in getBM(attributes = c("hgnc_symbol", "chromosome_name", "start_position", : Query ERROR: caught BioMart::Exception::Usage: Wrong format value for Start "*

My Input file format(positions.txt) start like below; chromosome_name startend 1 62920 16855942 1 16863509 16932568 ....

Would you advise to fix the error message? I appreciate for your help alot.

Thanks in advance!

Kelly

This seems to work for me if I run the following code based on your examples:

## Create example data.frame with genomic positions
positions <- data.frame(chromosome = c(1,1),
                        start = c(62920, 16863509),
                        end = c(16855942, 16932568))

## load package and set biomaRt dataset
library(biomaRt)
ensembl = useEnsembl(biomart='ensembl', 
                     dataset="hsapiens_gene_ensembl") 

## run query
results <- getBM(attributes = c("hgnc_symbol", "chromosome_name", "start_position", "end_position"), 
                 filters = c("chromosome_name", "start", "end"),
                 values = list(positions[,1], positions[,2], positions[,3]),
                 mart = ensembl)

I think for you're output you're running a much longer query than this with many more positions, and I wonder if biomaRt is doing something odd here.

Can you try running these commands, which will concatenate the chromosomal positions and use that in the query:

postions_combined <- apply(as.matrix(positions), 1, paste, collapse = ":")

results2 <- getBM(attributes = c("hgnc_symbol", "chromosome_name", "start_position", "end_position"), 
                 filters = c("chromosomal_region"),
                 values = postions_combined,
                 mart = ensembl)