SMMAT not reading grouping file

[alexisregelson]

This is my first time using SMMAT and I'm using sequencing data to run a rare variant test. I am using SMMAT to run a SKATO test.

When I run the code below, I get this error:
model0 <- glmmkin(Base_AD ~ sex, data = pheno, id = "iid", family = binomial(link = "logit"))

SMMAT(model0, group.file=genes, geno.file=snps, group.file.sep="\t", MAF.range=c(1e-7, 0.5), miss.cutoff=1, method="davies", tests=c("O", "E"))

Error in SMMAT(model0, group.file = genes, geno.file = snps, MAF.range = c(1e-07, :
Error: cannot read group.file!

Here is a snapshot of my grouping file:
1: HES4 1 999422 G GCT 1
2: HES4 1 999434 C T 1
3: HES4 1 999691 T C 1
4: HES4 1 999864 C A 1
5: GPR153 1 6253896 A ACC 1
6: ACOT7 1 6360600 T TC 1

UPDATE:
I played around with the example data and I get the same error when I load the grouping file (ie group.file) into R. So I then just supplied the path to my grouping file (genes) and now I get this error:

SMMAT(model0, group.file=genes, geno.file=snps, MAF.range=c(1e-7, 0.5), miss.cutoff=1, method="davies", tests=c("O", "E"))
Error in group.idx.start[i]:group.idx.end[i] : argument of length 0

Thank you!
Alexis

[hanchenphd]

Hi Alexis,

Thank you for your interest in SMMAT. Is your group file tab delimited or space delimited? By default SMMAT is expecting a tab delimited file, but you can change that using the argument group.file.sep.

Best,
Han

[alexisregelson]

Hello,

Yes, my group file is tab separated. Additionally, when I do add a separator argument to the SMMAT funciton, I get another error saying it cannot read the group file, which is the error I get when I actually load the file into R and try to run SMMAT.

Alexis

[hanchenphd]

Hi Alexis,

I am happy to take a look if you can send me a reproducible example.

Thanks,
Han

[alexisregelson]

Hi Han,

I've been able to reproduce the "Cannot read group.file" by using the SMMAT example data. If I read in SetID.withweights.txt instead of just referencing it's location, when I run SMMAT, I get the error. So I'm wondering if this is some kind of formatting issue with how the group file needs to be and how SMMAT reads it in R? I can work on getting a reprodicuble example for the other error I've gotten.

Thanks,
Alexis

[hanchenphd]

Hi Alexis,

You don't want to read in the group file by yourself. The function is expecting a file name for that argument. Please see the help document for details.

Best,
Han

[alexisregelson]

Hi Han,

I have figured out the issue, thanks for your help!

Alexis