Question: Using snpStats to read a pedfile, object 'm' not found
2
gravatar for nadrianam
2.1 years ago by
nadrianam30
nadrianam30 wrote:

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!

ped plink R • 941 views
ADD COMMENTlink modified 9 months ago by Kevin Blighe33k • written 2.1 years 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 2.1 years ago by ddiez1.7k

Were you able to get this fixed?

ADD REPLYlink written 11 months ago by Bioinformatics_NewComer320

I have the same error !!!!

ADD REPLYlink written 9 months ago by fatmasayed930
0
gravatar for Kevin Blighe
9 months ago by
Kevin Blighe33k
Republic of Ireland
Kevin Blighe33k 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: 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

ADD COMMENTlink written 9 months ago by Kevin Blighe33k
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