Closed thoree closed 2 years ago
kinshipLR complains about missing linkage map for a case with one marker. The problem goes away if the unnecessary call to transferMarkers is dropped. library(forrel)
kinshipLR
transferMarkers
library(ibdsim2) x = nuclearPed(1) pattern = ibdsim(x, 1, verbose = F) x = setSNPs(x, forrel::FORCE[1:2,]) id = c(1,3) H1 = profileSimIBD(x, pattern, ids = id, seed = 123)[[1]] H2 = list(singleton(id[1]), singleton(id[2])) H2 = transferMarkers(H1, H2, ids = id) kinshipLR(H1, H2, markers = 1)
linkageMap
Created on 2022-03-29 by the reprex package (v2.0.1)
Thanks, should be fixed now!
magnusdv
commented
2 years ago
kinshipLRcomplains about missing linkage map for a case with one marker. The problem goes away if the unnecessary call totransferMarkersis dropped. library(forrel)> Loading required package: pedtools
library(ibdsim2) x = nuclearPed(1) pattern = ibdsim(x, 1, verbose = F) x = setSNPs(x, forrel::FORCE[1:2,]) id = c(1,3) H1 = profileSimIBD(x, pattern, ids = id, seed = 123)[[1]] H2 = list(singleton(id[1]), singleton(id[2])) H2 = transferMarkers(H1, H2, ids = id) kinshipLR(H1, H2, markers = 1)
> Error: Linked markers detected, but no
linkageMapprovidedCreated on 2022-03-29 by the reprex package (v2.0.1)