invalid factor level, NA generated

[shameem356]

Hello,
I received below error while running the IntRegionalPlot code for my plant gwas result.please can you suggest me what is causing the error .

Error in [<-.data.frame(*tmp*, gene_snp[, j] == minor_allele, j, value = 0) :
missing values are not allowed in subscripted assignments of data frames
In addition: Warning message:
In [<-.factor(*tmp*, iseq, value = c(2, 2, 2, 2, 2, 2, 2, 2, :
invalid factor level, NA generated

Command :
IntRegionalPlot(chr=5,left=4683788-300000,right=4683788+300000,gtf=gtf,association=association,hapmap=hapmap,hapmap_ld =hapmap,threshold=5,leadsnp_size=2)

[shameem356]

Hello Team,

We are waiting for your valuable comments. Our hpamap file is having missing genotype (NN). Will 'IntAssoPlot' software allow missing genotype ?

[whweve]

NA are allowed in IntAssoPlot. As for the error, this might come from the wrong hapmap file format. You can look at our demo hapmap file, and find out the difference between files. Alternatively, you can send me some demo data. | | 王宏伟 | | ***@***.*** | 签名由网易邮箱大师定制 On 4/16/2021 ***@***.***> wrote： Hello, I received below error while running the code.please can you suggest me what is causing the error . Error in [<-.data.frame(*tmp*, gene_snp[, j] == minor_allele, j, value = 0) : missing values are not allowed in subscripted assignments of data frames In addition: Warning message: In [<-.factor(*tmp*, iseq, value = c(2, 2, 2, 2, 2, 2, 2, 2, : invalid factor level, NA generated Command : IntRegionalPlot(chr=5,left=4683788-300000,right=4683788+300000,gtf=gtf,association=association,hapmap=hapmap,hapmap_ld =hapmap,threshold=5,leadsnp_size=2) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[shameem356]

Hello Wang,

Thank you so much for your response. Here is the link for my demo data ( LG5)
https://wcmq.box.com/s/hvr4i8f668543mf7emwrzeeui3q7n9i1

Below is the code which I used to run the program:

hapmap1 <-read.table("LG5_LG_ID_trimmed_199sample_geno0.2_maf0.01_hwe10e6.hmp.txt",header = T,sep="\t")
gtf1<-read.table("LG_ID_Dec2020.gff3",sep="\t")
association1<-read.table("LG15_association_IntAssoPlot_a.txt",header = T,sep="\t")
IntRegionalPlot(chr=5,left=4683788-300000,right=4683788+300000,gtf=gtf1,association=association1,hapmap=hapmap1,leadsnp_size=3,threshold=5)

I appreciate your help

[shameem356]

Hello Wang,
My files are matching with demo data. I think the problem is with reading file. Please can you let me know if you are able to run the program with my data. I really appreciate your help.

[shameem356]

Awaiting for your response.

[vinod1981]

Dear Shameem,
I don't have an idea if you could solve the issue but it is a file issue in R, please change your gtf and hapmap file from factor to character level like this:
file %>% mutate_if(is.factor, as.character) -> file
And I hope after that it should work.
Thanks,
Vinod,

[shameem356]

Thanks Vinod. I will try your solution.