issue with check.missing

[fkgruber]

Hi,
I was trying to use your package and I'm getting the following error:
after typing:

pdata = load.plink.file("PlinkFiles/noout_75min_p.bed")
cdata = load.coord.file("coord2.txt")
raw.data <- check.missing(pdata, cdata)

I'm getting:

Error in .local(x, i, j, ..., drop) : 
  One or more row selections out of range

This is what pdata looks like:

> str(pdata)
List of 3
 $ genotypes:Formal class 'SnpMatrix' [package "snpStats"] with 1 slot
  .. ..@ .Data: raw [1:90, 1:7667] 03 03 03 03 ...
  .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. ..$ : chr [1:90] "101156" "101157" "101160" "101164" ...
  .. .. .. ..$ : chr [1:7667] "locus_12958:1" "locus_27912:1" "locus_30206:1" "locus_35978:1" ...
 $ fam      :'data.frame':	90 obs. of  6 variables:
  ..$ pedigree: chr [1:90] "101156" "101157" "101160" "101164" ...
  ..$ member  : chr [1:90] "101156" "101157" "101160" "101164" ...
  ..$ father  : logi [1:90] NA NA NA NA NA NA ...
  ..$ mother  : logi [1:90] NA NA NA NA NA NA ...
  ..$ sex     : logi [1:90] NA NA NA NA NA NA ...
  ..$ affected: logi [1:90] NA NA NA NA NA NA ...
 $ map      :'data.frame':	7667 obs. of  6 variables:
  ..$ chromosome: int [1:7667] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ snp.name  : chr [1:7667] "locus_12958:1" "locus_27912:1" "locus_30206:1" "locus_35978:1" ...
  ..$ cM        : logi [1:7667] NA NA NA NA NA NA ...
  ..$ position  : int [1:7667] 1 1 1 1 1 1 1 1 1 1 ...
  ..$ allele.1  : chr [1:7667] "A" "T" "G" "C" ...
  ..$ allele.2  : chr [1:7667] "G" "C" "A" "T" ...

and this is what the cdata looks like:

str(cdata)
'data.frame':	90 obs. of  4 variables:
 $ id       : int  113582 103263 91917 113566 92127 101156 101157 113574 113576 103210 ...
 $ latitude : num  -23.1 -23 -22.9 -23 -22.9 ...
 $ longitude: num  119 119 119 119 119 ...
 $ region   : chr  "region_1" "region_1" "region_1" "region_1" ...

[BenjaminPeter]

hmm, I wonder if the type mismatch between coordinate file ids (int) and genotypes (pdata$genotype) (str) is the issue. If so, the recent commit should have fixed that, would you mind trying it?

[fkgruber]

thanks
I ended up fixing the mismatch. It seems that there was a sample with a different id in the genotype