Using snpStats to read a pedfile, object 'm' not found

Question

[nadrianam]

Hello,

I'm using snpStats on R to try and read a pedfile and keep running into an issue.

I input this:

> read.pedfile("test.ped")

And get this:

Error in read.pedfile("test.ped") : object 'm' not found

Any idea what 'm' is? I imagine it's a type of variable in the script that converts my file to a snpMatrix but I'm really new to R so I'm not sure how to go about trying to fix it. Thanks!

[ddiez]

It might be a bug in the software (that variable name is used indeed in read.pedfile) but it is difficult to say. Your best chance is report this at the bioconductor support site or contact the author maintainer directly.

[Bioinformatics_NewComer]

Were you able to get this fixed?

[fatmasayed93]

I have the same error !!!!

Answer 1

[Kevin Blighe]

This question just popped up due to fatmasayed93's comment (above). The solution is to not use snpStats - I also had trouble with it.

I wrote my own code in R that can read in PLINK data and that then performs different types of regression analyses, in my case conditional logistic regression on trios: https://github.com/kevinblighe/GwasTriosCLogit

Unfortunately this is not tailoured for general use, so, you will have to follow my code line by line and modify it as needed. It does everything that snpStats can do, though, plus extra.

Kevin