Error in if (lev[1] != inter) { : the condition has length > 1

[grtomam1]

In the latest version of GAPIT I have been getting this error message "Error in if (lev[1] != inter) { : the condition has length > 1" while trying to numericalize the hapmap file.

The same input files are not giving this error in an older version of GAPIT. Also the version giving an error is installed on a HPC. I am one of two people I know having this issue. I have tried both R 4.3.0 and 4.4.0

[jiabowang]

Yes, some functions were needed to update above R 4.4.0.
Now we have fixed this BUG, please re-source GAPIT function and try again.

[Eason418]

Yes, some functions were needed to update above R 4.4.0. Now we have fixed this BUG, please re-source GAPIT function and try again.

您好，我的R版本是4.4.0，GAPIT版本是GAPIT_3.4.0，依然是同样的报错，请问如何解决这个报错？

[Eason418]

报错信息如下：

[jiabowang]

@Eason418 请使用最新的GAPIT， 现在是3.5版本，或者从GitHub上下载GAPIT.Numericalization函数，本地source一下

[ShonaStrachan]

Hello,
I've tried using your fix and still get the same error as Eason418. I was using R 4.4.0 and GAPIT 3.5. Tried re-sourcing GAPIT as well as going back to an older version - nothing seems to fix it.

[jiabowang]

@ShonaStrachan Could you send your data with me? So I can help.

[ShonaStrachan]

gwas-ready.hmp.txt
gwas-phenotype.txt

[jiabowang]

@ShonaStrachan Thanks for your data. I noticed that there are lots of multiple mutations in your genotype file. we call them as MNPs, not as SNPs. So GAPIT can not deal with this type data directly.

We designed another function for this type data recently. Below is code.

X=myG[-1,]
newG=NULL
for(i in 1:nrow(X))
{
Gstore=GAPIT.HMP.Amplification(X[i,])
newG=rbind(newG,Gstore)
if(i%%100==0)print(i)
}
newG=rbind(myG[1,],newG)
write.table(newG,"new.HapMap.txt",sep="\t",row.names=F,quote=F,col.names=F)

myG=data.table::fread("new.HapMap.txt",
header = F,
na.strings = c("NA", "NaN"),
data.table = F)
myGAPIT <- GAPIT(
G=myG,#Genotype
PCA.total=3)

write.table(myGAPIT$GD,"GD.txt",row.names=F,quote=F)
write.table(myGAPIT$GM,"GM.txt",row.names=F,quote=F)
write.table(myGAPIT$PCA,"CV.txt",row.names=F,quote=F)
myGD=myGAPIT$GD
myGM=myGAPIT$GM
myCV=myGAPIT$PCA
After got the numeric genotype data, you can use them to do GWAS.

[ShonaStrachan]

I've tried the fix and it's working now. Thank you for your help.