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merns / postgwas

postgwas package for R
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regionalplot problem #1

Open sab13 opened 7 years ago

sab13 commented 7 years ago

Hi,

I'm using postgwas package to visualize GWAS data. When I'm using regionalplot function I've this error msg Reading GWAS datasets ... PLINK format detected Assembling regions... Initializing biomart connection (SNPs)... Retrieving gene (and exon) information... Initializing biomart connection (genes)... Extracting SNPs for LD computation: Retrieving genotypes from HapMart... Error in read.table(query.url, col.names = c("CHR", "SNP", "BP")) : more columns than column names

I've changed the biomart.config as following myconfig <- biomartConfigs$hsapiens myconfig$gene$host <- "grch37.ensembl.org" myconfig$gene$mart <- "ENSEMBL_MART_ENSEMBL" myconfig$snp$host <- "grch37.ensembl.org" myconfig$snp$mart <- "ENSEMBL_MART_SNP"

and my R commandline is: regionalplot(snps, test2, biomart.config = myconfig, window.size = 400000, draw.snpname = data.frame( snps = c("rs1532625", "rs247617"), text = c("rs1532625", "rs247617"), angle = c(20, 160), length = c(1, 1), cex = c(0.8) ), ld.options = list( gts.source = 2, max.snps.per.window = 2000, rsquare.min = 0.8, show.rsquare.text = FALSE ), out.format = list(file = NULL, panels.per.page = 2))

And my test2 dataframe has 4 columns (CHR, P, SNP, BP) image

I really don't know how to resolve this pb. I will be realy thanksfull for some help.

Facenomore23 commented 6 years ago

Hello,

I have the same problem as you. I think that it is due to a wrong url. The function regionalplot was requesting information from Hapmap data set on the site NCBI. But NCBI does no more provide it since June 16, 2016.

Did you managed to resolve it or to find a different package to do a regional plot ?

bambrozio commented 4 years ago

Hi @facenomore23 and @sab13! Any update? I'm in the same boat. Please, let me know if you found a solution. Thanks!