I have been trying to run a GWAS using GAPIT and I keep getting this error:
> # Import data from Zhiwu Zhang Lab
> myZZY <- read.table("http://zzlab.net/GAPIT/data/mdp_traits.txt", head = TRUE)
> myZZGD <- read.table(file = "http://zzlab.net/GAPIT/data/mdp_numeric.txt", head = TRUE)
> myZZGM <- read.table(file = "http://zzlab.net/GAPIT/data/mdp_SNP_information.txt", head = TRUE)
> # GWAS
> myGAPIT <- GAPIT(
+ Y = myZZY[, c(1, 2, 3)], # first column is ID
+ GD = myZZGD,
+ GM = myZZGM,
+ PCA.total = 3,
+ model = c("FarmCPU", "Blink"),
+ Multiple_analysis = TRUE
+ )
[1] "--------------------- Welcome to GAPIT ----------------------------"
[1] "FarmCPU" "Blink"
[1] "--------------------Processing traits----------------------------------"
[1] "Phenotype provided!"
[1] "The 1 model in all."
[1] "FarmCPU"
[1] "GAPIT.DP in process..."
[1] "GAPIT will filter marker with MAF setting !!"
[1] "The markers will be filtered by SNP.MAF: 0"
maf_index
TRUE
3093
[1] "Calling prcomp..."
[1] "Creating PCA graphs..."
[1] "Joining taxa..."
[1] "Exporting PCs..."
[1] "PC created"
[1] "Filting marker for GAPIT.Genotype.View function ..."
Error in layout.matrix(mat = layout.matrix, heights = c(100, 80, 120), :
argument "p" is missing, with no default
In addition: There were 50 or more warnings (use warnings() to see the first 50)
So far I have tried the following:
I have tried the following to solve it so far:
- I ran the example data from the GAPIT manual and had the same issue which is the code above
- I double checked the structures of myY, myGD and myGM against the example and they seem the same
> str(myY)
'data.frame': 2559 obs. of 2 variables:
$ taxa : chr "XYZ" "ABC" "123" "EFG" ...
$ Blues: num 659 638 620 715 652 ...
> str(myGM) ###Allele ID is character, Chr and Pos = numeric - use code below
'data.frame': 13678 obs. of 3 variables:
$ Marker: chr "6178219|F|0-66:T>C-66:T>C" "6154603|F|0-43:C>T-43:C>T" "6194871|F|0-43:G>A-43:G>A" "6186111|F|0-6:G>A-6:G>A" ...
$ Chr : num 12 5 5 1 11 8 12 1 9 8 ...
$ Pos : num 4636524 15568186 15584805 7403652 18283519 ...
> str(myGD)
'data.frame': 1759 obs. of 13679 variables:
$ taxa : chr "XYZ" "ABC" "123" "EFG" ...
$ 6178219|F|0-66:T>C-66:T>C : num 0 0 1 0 2 0 0 0 2 0 ...
$ 6154603|F|0-43:C>T-43:C>T : num 0 0 1 0 0 0 0 0 2 0 ...
- I had also cleaned the marker and genotype names, removing |,-,:,> . This did not seem to matter in the GAPIT manual or the video example.
- Last thing I tried was converting myY, myGD and myGM to matrixes and that still resulted in the same error. I have set these back to normal to keep them the same as the other two scripts I am going between.
Thank you so much for any advice you can provide