Question: Reading a .ped file in R?
gravatar for nadrianam
3.0 years ago by
nadrianam30 wrote:

I apologize if this is incredibly asinine, but how can I view my ped file as a matrix in R? I've been using plink to do some analyses on a bunch of chip-seq data we have, but we want to separate the cases from the two studies that make up our dataset. I plan on utilizing some sort of "if, else" function for the actual sorting, but I need to be able to view the Individual IDs in order to write that line of code.

1- What package should I install to do this?

2- What function lets me view my file in a matrix?

I'm running R version 3.3.1 and some of the more popular package options according to Google don't seem to work with my version (SNPRelate, SNPStats). I have downloaded genetics and GenAbel but I don't seem to be able to pull my file up in the way I wish to view it.

Thanks in advance!

ped plink R • 3.9k views
ADD COMMENTlink modified 20 months ago by fatmasayed930 • written 3.0 years ago by nadrianam30

The snpStats package is in Bioconductor 3.4, which works with R-3.3.1.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by ddiez1.8k

The function read.pedfile() from package trio in Bioconductor can help you read in a .ped file in R.

ADD REPLYlink written 2.4 years ago by miaowzai170
gravatar for fatmasayed93
20 months ago by
fatmasayed930 wrote:

Did you find the answer to your question?

ADD COMMENTlink written 20 months ago by fatmasayed930
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