Question: Using snpStats to read a pedfile, object 'm' not found
gravatar for nadrianam
22 months ago by
nadrianam30 wrote:


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!

ped plink R • 863 views
ADD COMMENTlink modified 6 months ago by Kevin Blighe28k • written 22 months ago by nadrianam30

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.

ADD REPLYlink written 22 months ago by ddiez1.7k

Were you able to get this fixed?

ADD REPLYlink written 8 months ago by Bioinformatics_NewComer310

I have the same error !!!!

ADD REPLYlink written 6 months ago by fatmasayed930
gravatar for Kevin Blighe
6 months ago by
Kevin Blighe28k
USA / Europe / Brazil
Kevin Blighe28k wrote:

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:

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.


ADD COMMENTlink written 6 months ago by Kevin Blighe28k
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