[BioC] GWASTools mendelList Constructor

Samuel Younkin syounkin at jhsph.edu
Wed Sep 12 16:36:58 CEST 2012


I am trying to use the Mendelian error checking feature of the 
Bioconductor package GWASTools.  When I try to create a mendelList 
object using the constructor function mendelList(), it consistently 
returns NULL with no warning or error message.

I have tried changing the subject ids to character, or integer, or 
numeric, but I continue to get NULL.  Without any error message to work 
with I am at a loss.  Any advice?

Should the offspring, mother and father vectors be scan ids or 
scan/subject names?  My scan names are not numbers and so these vectors 
would not satisfy the requirement in the manual of "a vector of 
offspring/father/mother ID numbers."

Should the scanID vector be the scan id of the offspring?

Any advice would be greatly appreciated.



 > sessionInfo()
R version 2.15.1 Patched (2012-07-01 r59713)
Platform: x86_64-unknown-linux-gnu (64-bit)

  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
  [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
  [7] LC_PAPER=C                     LC_NAME=C
  [9] LC_ADDRESS=C                   LC_TELEPHONE=C

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

other attached packages:
  [1] MinimumDistance_1.1.20 CleftCNVAssoc_0.0.1    GenomicRanges_1.9.63
  [4] IRanges_1.15.43        GWASTools_1.2.1        sandwich_2.2-9
  [7] zoo_1.7-7              GWASExactHW_1.0        ncdf_1.6.6
[10] Biobase_2.17.6         BiocGenerics_0.3.1     BiocInstaller_1.4.7

loaded via a namespace (and not attached):
  [1] affyio_1.25.0         annotate_1.35.3       AnnotationDbi_1.19.35
  [4] Biostrings_2.25.8     bit_1.1-8             codetools_0.2-8
  [7] crlmm_1.15.18         DBI_0.2-5             DNAcopy_1.31.1
[10] ellipse_0.3-7         ff_2.2-7              foreach_1.4.0
[13] genefilter_1.39.0     grid_2.15.1           iterators_1.0.6
[16] lattice_0.20-6        lmtest_0.9-30         msm_1.1.1
[19] mvtnorm_0.9-9992      oligoClasses_1.19.41  preprocessCore_1.19.0
[22] RSQLite_0.11.1        SNPchip_2.3.13        splines_2.15.1
[25] stats4_2.15.1         survival_2.36-14      tools_2.15.1
[28] VanillaICE_1.19.23    XML_3.9-4             xtable_1.7-0
[31] zlibbioc_1.3.0

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