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JiscaH / sequoia

R package for pedigree inference based on SNP data
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Silly question for a very usefull package #2

Closed jblamyatifremer closed 7 years ago

jblamyatifremer commented 7 years ago

Hi Jisca,

I am sure that you have a R trick to access to dam object stored in compareOUT$Counts...

get assignation statistic for dam

compareOUT <- PedCompare(Ped1=ped1,Ped2=SeqOUT$Pedigree) dam <- compareOUT$Counts[1] ## NOT WORKING dam <- unlist(compareOUT$Counts)[1] ## NOT WORKING

best regards,

JB

JiscaH commented 7 years ago

Hello,

There are no stupid questions! (only not-sufficiently-clear help files...)

compareOUT$Counts is what R calls an 'array', and you get the dam part as dam <- compareOUT$Counts[, , "dam"] # or dam <- compareOUT$Counts[, , 1]

Glad you find the package useful! Out of personal curiosity - what species are you working on?

cheers, Jisca

On 17/07/2017 17:49, jblamyatifremer wrote:

Hi Jisca,

I am sure that you a R trick to access to dam object stored in compareOUT$Counts...

get assignation statistic for dam

compareOUT <- PedCompare(Ped1=ped1,Ped2=SeqOUT$Pedigree) dam <- compareOUT$Counts[1] ## NOT WORKING dam <- unlist(compareOUT$Counts)[1] ## NOT WORKING

best regards,

JB

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jblamyatifremer commented 7 years ago

Perfect ! I am working on oysters (successive hermaphrodite) populations or bi-parental cross. Most of the time, we do have an observed pedigree, and we are now accumulating HTS data. I am measuring the amount of putative errors in the observed pedigree. I am also planning to use your package to design lower snp panel density for assignations, imputations from public array.
I close this thread. Thanks you again for your time.