Question: Error when computing ld with snpStats in big samples
gravatar for carlos.ruiz
2.1 years ago by
carlos.ruiz0 wrote:


I want to compute the linkage disequilibrium between the SNPs of some predifined regions of the genome of around Mb using snpStats. I have downloaded 1000 Genomes VCF files but I am experiencing some errors.

I start with a list of target genomic regions in a GRanges. I have created some functions to read the SNPs of the region, transform the VCF object into a SNP matrix and finally compute the LD. Most of these steps are performed using existing BioC functions. The problems appear when I want to compute the LD for a big numbers of SNPs with a big depth.

I tried to compute the LD using the ld function of snpStats and the following problem raised:

> computeLD(GRcomp[2], EUR))

*** caught segfault ***
address 0x7fe323878000, cause 'invalid permissions'

 1: .Call("ld", x, y, as.integer(depth), cstats, symmetric, PACKAGE = "snpStats")
 2: ld(snpsVCF$genotypes, depth = 30000, stats = "")

3: computeLD(GRcomp[2], EUR)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace

This region is quite big (14Mb) and contains many snps (379737)

>  as.character(GRcomp[2])

This is an example of a very big region but I have had problems with smaller regions too. I have tested the wrappers with smaller regions and it works. Is there any limitation in the maximum of SNPs and depth that can be passed to ld? I haven't been able to find anything about it on the web.

I also send you the code of my wrappers. The functions use VCF files of 1000 Genomes:

computeLD <- function(range, samples){
  message("Loading VCF")
  snpsVCF <- getVCFmatrix(range, samples)
  message("Computing LD")
  res <- ld(snpsVCF$genotypes, depth = 30000, stats = "")

getVCFmatrix <- function(range, samples = vcfsamples){
  vcf <- loadVCFrange(range, samples)
  snpsVCF <- genotypeToSnpMatrix(vcf)
  ## Conversion from VCF to SNP matrix produces some SNPs to be NA (multiallelic or bigger than 1)
  snpsVCF$map$position <- start(rowRanges(vcf))
  snpsVCF$map$chromosome <- rep(as.character(seqnames(range)), nrow(snpsVCF$map))
  snpsVCF$genotypes <- snpsVCF$genotypes[, !snpsVCF$map$ignore]
  snpsVCF$map <- snpsVCF$map[!snpsVCF$map$ignore, ]
  snpsVCF$map$allele.2 <- unlist(snpsVCF$map$allele.2)

loadVCFrange <- function(range, samples){
  vcffile <- paste0("ALL.chr", as.character(seqnames(range)), ".phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz")
  vcfsamples <- samples(scanVcfHeader(vcffile))
  samples <- vcfsamples[vcfsamples %in% samples]
  param <- ScanVcfParam(samples = samples, which = range)
  vcf <- readVcf(vcffile, "hg19", param)

I also send you my session info:

R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

 [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] snpStats_1.22.0            Matrix_1.2-6
 [3] survival_2.39-4            VariantAnnotation_1.18.1
 [5] SummarizedExperiment_1.2.2 Biobase_2.32.0
 [7] ggplot2_2.1.0              Rsamtools_1.24.0
 [9] Biostrings_2.40.1          XVector_0.12.0
[11] GenomicRanges_1.24.1       GenomeInfoDb_1.8.1
[13] IRanges_2.6.0              S4Vectors_0.10.1
[15] BiocGenerics_0.18.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.5             AnnotationDbi_1.34.3    splines_3.3.0
 [4] GenomicAlignments_1.8.1 zlibbioc_1.18.0         munsell_0.4.3
 [7] BiocParallel_1.6.2      lattice_0.20-33         BSgenome_1.40.0
[10] colorspace_1.2-6        plyr_1.8.3              tools_3.3.0
[13] grid_3.3.0              gtable_0.2.0            DBI_0.4-1
[16] rtracklayer_1.32.0      bitops_1.0-6            biomaRt_2.28.0
[19] RCurl_1.95-4.8          RSQLite_1.0.0           GenomicFeatures_1.24.2
[22] scales_0.4.0            XML_3.98-1.4


Carlos Ruiz

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