Deleted:Tabix file download error eQTL analysis
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4 months ago
v.johnson ▴ 20

I am trying to download a tabix file to perform an analysis on an eQTL dataset, however I have the following error each each file I try to try from the eQTL - catalogue

library(ggplot2)
library(readr)
library(coloc)
library(GenomicRanges)
library(seqminer)

tabix_paths = read.delim("https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths.tsv", 
                         sep = "\t", 
                         header = TRUE, stringsAsFactors = FALSE) %>% dplyr::as_tibble()
imported_tabix_paths = read.delim("https://raw.githubusercontent.com/eQTL-Catalogue/eQTL-Catalogue-resources/master/tabix/tabix_ftp_paths_imported.tsv", 
                                  sep = "\t", header = TRUE, stringsAsFactors = FALSE) %>% dplyr::as_tibble()

import_eQTLCatalogue <- function(ftp_path, region, selected_gene_id, column_names, verbose = TRUE){

  if(verbose){
    print(ftp_path)
  }

  #Fetch summary statistics with seqminer
  fetch_table = seqminer::tabix.read.table(tabixFile = ftp_path, tabixRange = region, stringsAsFactors = FALSE) %>%
    dplyr::as_tibble()
  colnames(fetch_table) = column_names

  #Remove rsid duplicates and multi-allelic variant
  summary_stats = dplyr::filter(fetch_table, gene_id == selected_gene_id) %>%
    dplyr::select(-rsid) %>% 
    dplyr::distinct() %>% #rsid duplicates
    dplyr::mutate(id = paste(chromosome, position, sep = ":")) %>% 
    dplyr::group_by(id) %>% 
    dplyr::mutate(row_count = n()) %>% dplyr::ungroup() %>% 
    dplyr::filter(row_count == 1) #Multialllics
}

region = "3:56615721-57015721"
platelet_df = dplyr::filter(tabix_paths, study == "CEDAR", tissue_label == "platelet")

#Extract column names from first file
column_names = colnames(readr::read_tsv(platelet_df$ftp_path, n_max = 1))

#Import summary statistics
summary_stats = import_eQTLCatalogue(platelet_df$ftp_path, region, selected_gene_id = "ENSG00000163947", column_names)

    [1] "ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/CEDAR/microarray/CEDAR_microarray_platelet.all.tsv.gz"

    Cannot open specified tabix file: ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/CEDAR/microarray/CEDAR_microarray_platelet.all.tsv.gz
    Cannot open specified tabix file: ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/CEDAR/microarray/CEDAR_microarray_platelet.all.tsv.gz
    Error in strsplit(body, "\t") : non-character argument
    Called from: strsplit(body, "\t")
    Browse[1]> Q
    > platelet_df$ftp_path
    [1] "ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv/CEDAR/microarray/CEDAR_microarray_platelet.all.tsv.gz"

I am not sure what the problem relates to? Any advice would be amazing!

download R eQTL tabix error • 228 views
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