Hi everyone! I'm having a problem with package kinship2 to conduct a pedigree analysis, and I found nothing about it on google. I get this error trying to run this command:

ped2 <- with(pedigree(id, momid, dadid, sex))

Error in pedigree(id, momid, dadid, sex) : object 'id' not found

This is how my ped file look like:

famid id dadid momid sex pheno

EPBL-0001 0200356041 0200356061 0200356051 2 0

EPBL-0001 0200356051 0 0 2 0

EPBL-0001 0200356061 0 0 1 0

EPBL-0004 0200356071 0200356091 0200356081 2 0

EPBL-0004 0200356081 0 0 2 0

EPBL-0004 0200356091 0 0 1 0

Prior to this I run:

pedall <- pedigree(id= multisample_headers$id, dadid = multisample_headers$dadid, momid = multisample_headers$momid, sex= multisample_headers$sex, famid = multisample_headers$famid)

And it works telling me that the pedigree list contain 83 subjects in 28 families.

What's the problem with the id? Thank you in advance.

I believe its looking for the id as a defined variable. id, momid, dadid, sex are arguments to the function and need to be defined; if there are not assigned variables the same name as those it will not be able to find it. Based on the other command you showed I would assume you would want to update the call to something

ped2 <- with(pedigree(id=multisample_headers$id, momid=multisample_headers$momid, dadid=multisample_headers$dadid, sex=multisample_headers$sex))

Or alternatively if you know you will be using those values multiple times, you could define them as variables

id=multisample_headers$id
momid=multisample_headers$momid
dadid=multisample_headers$dadid
sex=multisample_headers$sex)

# then this should work 
ped2 <- with(pedigree(id, momid, dadid, sex))