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Fix twin matrix size mismatch between addtwins and merging methods #119

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Merged
smasongarrison merged 2 commits into from
Feb 13, 2026
Merged

Fix twin matrix size mismatch between addtwins and merging methods #119

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021e8fd
Fix twin matrix size mismatch between addtwins and merging methods
claude Feb 13, 2026
006d675
Merge branch 'mztwins' into claude/fix-twin-matrix-sizes-bnNVe
smasongarrison Feb 13, 2026
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8 changes: 6 additions & 2 deletions R/buildComponent.R
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Original file line number Diff line number Diff line change
Expand Up @@ -147,7 +147,7 @@ ped2com <- function(ped, component,
if (mz_method %in% c("merging") && mz_twins == TRUE && !is.null(mz_pairs) && length(mz_pairs) > 0) {
# replace all MZ twin IDs with the first twin's ID in each pair so they are merged for the path tracing and all subsequent steps. We will copy the values back to the second twin at the end.

for (id_pair in mz_pairs) {
for (id_pair in mz_id_pairs) {
twin1_id <- id_pair[1]
twin2_id <- id_pair[2]
twin2_row <- which(ped$ID == twin2_id)
Expand Down Expand Up @@ -387,7 +387,11 @@ ped2com <- function(ped, component,
# Assign 1 to all nonzero elements for mitochondrial component
}

if (config$sparse == FALSE) {
# Remove explicit zeros so that both mz_method paths produce
# structurally identical sparse matrices
if (config$sparse == TRUE) {
r <- Matrix::drop0(r)
} else {
r <- as.matrix(r)
}
# flattens diagonal if you don't want to deal with inbreeding
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