Errors when attempting to run association tests in GWASTools
Entering edit mode
mrynerson • 0
Last seen 6.3 years ago
United States


I am attempting to do an association analysis with GWASTools. I have followed the example script for making the GenotypeData object, and when I call variables with get__() I see exactly what I would expect. I am using imputed genotypes. The genotype file that I am working with is only a small subset of chromosome 1 (I wanted to troubleshoot with a small dataset before scaling up), and the phenotype includes only males, although there are females in the file. Females just have NA for all phenotypes except sex. When I call getSex(), I see a vector of Ms and Fs as I would expect. 

My R commands are listed below:

ncfile <- tempfile()
snpfile <- tempfile()
scanfile <- tempfile()
probfile <- file.path("/path1/dcct_1kg_chr1_1_0")
sampfile <- file.path("/path2/EDcph.sample") 

ncdfImputedDosage(input.files=c(probfile,sampfile), ncdf.filename=ncfile,chromosome=1, input.type="IMPUTE2",input.dosage=FALSE,
                  snp.annot.filename=snpfile, scan.annot.filename=scanfile, verbose=TRUE)
nc <- NcdfGenotypeReader(ncfile)
scanAnnot <- getobj(scanfile)
snpAnnot <- getobj(snpfile)
genoData <- GenotypeData(nc,scanAnnot=scanAnnot, snpAnnot=snpAnnot) 

# Two different association tests give me different errors, which makes me think something is wrong with the GenotypeData object, but I can't figure out what:

> assocTestCPH(genoData, event="pheno","time_to_event", covars=c("Age"),
               + chromosome.set = 1, block.size=500, verbose=TRUE, outfile="try_cph.out")
 Error in `[<-`(`*tmp*`, sample.dat$sex == "F", YchromCode(genoData), value = FALSE) : 
     subscript out of bounds

> mydat <- assocTestRegression(genoData, outcome="pheno", model.type="logistic", dosage=TRUE)
Determining chromosome and SNP information...
Gene action check...
Covariate check...
Interaction Variable check...
Models checks...
Determining number of SNP blocks for Chromosome 1 ...
Determining which Scans to keep for Chromosome 1 ...
Beginning calculations for Chromosome 1 ...
Error in R_nc_inq_varndims: NetCDF: Not a valid ID
Error in varndims.ncdf(nc, varid) : error returned from C call


Here is the sessionInfo:

R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] GWASTools_1.10.1    sandwich_2.3-2      gdsfmt_1.1.0.1      ncdf_1.6.8          Biobase_2.24.0      BiocGenerics_0.10.0

loaded via a namespace (and not attached):
 [1] DBI_0.3.1          DNAcopy_1.38.1     grid_3.1.1         GWASExactHW_1.01   lattice_0.20-29    lmtest_0.9-33      quantsmooth_1.30.0 RSQLite_0.11.4     splines_3.1.1      survival_2.37-7   
[11] tools_3.1.1        zoo_1.7-11  


I would greatly appreciate any suggestions.

-Melody Palmer, University of Washington Dept of Urology,

gwastools • 938 views
Entering edit mode
Last seen 11 weeks ago
University of Washington

Hi Melody,

There was a bug in assocTestCPH when using a dataset with no Y chromosome, but it has been fixed in the latest release.  Please upgrade to GWASTools 1.12.0 and see if that solves your problem.

The second error with assocTestRegression looks like a problem reading from the netCDF file, and I suspect it is the result of an error state introduced by the previous failed call to assocTestCPH.  Try again with a fresh R session and see if the error goes away.



Entering edit mode
mrynerson • 0
Last seen 6.3 years ago
United States

Hi Stephanie,

 Thank you so much! I thought I had updated everything, but apparently not. Now it's working.



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