Hi,
I was wondering if anyone could help me address this issue? I am trying to use the treeWAS package on R to perform SNP analysis. I have prepared my two data-sets (one is a matrix (geney) the other is factor (pheny)) as required by the package, and then ran the following treeWAS command. I keep getting the "Error in axis" comment below:
> out <- treeWAS(snps = geney,
+ phen = pheny,
+ na.rm=TRUE,
+ tree = "BIONJ",
+ seed = 1)
Error in axis(side = side, at = x, labels = lab, ...) :
no locations are finite
When I use the two example data-sets, provided with the package, the command works fine. I have checked the two data-sets I have created against the two examples in the package and the class, attributes and formatting match. So I'm not sure what the error means. The following is a short description of my data:
> class(geney)
[1] "matrix"
> str(geney)
num [1:27, 1:62] NA NA NA NA NA 0 NA NA NA NA ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:27] "FR3883.vcf" "FR3977.vcf" "FR4887.vcf" "FR4928.vcf" ...
..$ : chr [1:62] "X1000756.G" "X1000756.t" "X1001126.g" "X1001126.T" ...
> class(pheny)
[1] "factor"
> str(pheny)
Factor w/ 2 levels "A","B": 1 1 1 1 1 1 1 1 1 1 ...
- attr(*, "names")= chr [1:27] "FR4887.vcf" "FR4928.vcf" "FR4930.vcf" "FR5128.vcf" ...
This is the description of the exemplary data-sets:
> class(snps)
[1] "matrix"
> str(snps)
num [1:100, 1:20003] 0 1 1 1 1 1 1 1 1 1 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:100] "A_1090" "B_1078" "A_1070" "B_1083" ...
..$ : chr [1:20003] "1.g" "1.a" "2.t" "2.g" ...
> class(phen)
[1] "factor"
> str(phen)
Factor w/ 2 levels "A","B": 2 2 2 2 1 2 1 1 2 2 ...
- attr(*, "names")= chr [1:100] "B_1132" "B_1105" "B_1079" "B_1133" ...
I'm not sure if this is an R issue or a treeWAS issue. Any feedback would be greatly appreciated!
Cheers =)
