glmm.wald exporting only NA
Closed this issue · 5 comments
Hello,
For some reason "glmm.wald" is exporting only NA when I provide the inputs below. I'm not sure where my error is.
Thank you,
Neal
snps<-c("Chr01K_671719","Chr01K_676401","Chr01K_676418","Chr01K_676677","Chr01K_676813")
glmm.wald(fixed = trt ~ 1, data = y, kins = K, id = "ID",verbose=T,snp.col=1,
family = quasibinomial(link = "logit"), infile = "tmp_infile.txt", snps=snps,
infile.nrow.skip = 0, infile.ncol.skip = 1, infile.ncol.print = 1,infile.sep = ",")
Oh, for reference, it's returning a correctly formatted data frame of NAs.
Can you share your log file and output?
Thanks,
Han
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[Workspace loaded from ~/Desktop/.RData]
library(GMMAT)
#some data processing that I deleted
tmp[1:5,1:5] #marker array (dosage of DNA pools)
A113.0 A113.1 A203.0 A203.1 A204.0
Chr01K_671719 1.808000 1.982456 1.927007 1.765625 1.280000
Chr01K_676401 1.789474 1.647059 1.333333 1.750000 1.739130
Chr01K_676418 1.866667 1.833333 1.250000 1.727273 1.809524
Chr01K_676677 2.000000 2.000000 1.333333 2.000000 1.833333
Chr01K_676813 1.238095 1.809524 1.813953 1.931034 1.735849
write.csv(tmp,"tmp_infile.txt",row.names = T)
outfile<-"outout.txt"
snps<-c("Chr01K_671719","Chr01K_676401","Chr01K_676418","Chr01K_676677","Chr01K_676813")
glmm.wald(fixed = trt ~ 1, data = y, kins = K, id = "ID",verbose=T,snp.col=1,
-
family = quasibinomial(link = "logit"), infile = "tmp_infile.txt", snps=snps, -
infile.nrow.skip = 0, infile.ncol.skip = 1, infile.ncol.print = 1,infile.sep = ",")
Progress of Wald test:
| | 0%
Analyze SNP 1 : Chr01K_671719
|================== | 20%
Analyze SNP 2 : Chr01K_676401
|==================================== | 40%
Analyze SNP 3 : Chr01K_676418
|====================================================== | 60%
Analyze SNP 4 : Chr01K_676677
|======================================================================== | 80%
Analyze SNP 5 : Chr01K_676813
|==========================================================================================| 100%
SNP N AF BETA SE PVAL converged
1 Chr01K_671719 NA NA NA NA NA NA
2 Chr01K_676401 NA NA NA NA NA NA
3 Chr01K_676418 NA NA NA NA NA NA
4 Chr01K_676677 NA NA NA NA NA NA
5 Chr01K_676813 NA NA NA NA NA NA
Warning message:
In glmm.wald(fixed = trt ~ 1, data = y, kins = K, id = "ID", verbose = T, :
Argument select is unspecified... Assuming the order of individuals in infile matches unique id in data...
str(y)
'data.frame': 60 obs. of 3 variables:
$ pop : chr "113" "113" "203" "203" ...
$ trt : Factor w/ 2 levels "0","1": 1 2 1 2 1 2 1 2 1 2 ...
$ ID : chr "A113.0" "A113.1" "A203.0" "A203.1" ...
If the first row of your infile includes the ID's, you need to specify infile.nrow.skip = 1.
Also you might need to add quote = FALSE in write.csv.
Best,
Han
Good ideas, quote = FALSE in write.csv fixed it. Thank you for your time.