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" ...
Hi,
I was trying to use your package and I'm getting the following error:
after typing:
I'm getting:
This is what pdata looks like:
and this is what the cdata looks like: