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Fix SIC extraction for cell types with shared prefixes #6

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Merged
jeliason merged 3 commits into from
Feb 4, 2026
Merged

Fix SIC extraction for cell types with shared prefixes #6

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690d7bf
Fix SIC extraction failing when cell type names are prefixes of others
jeliason Feb 3, 2026
354aab1
Fix macOS CI by using upgrade: TRUE for R dependencies
jeliason Feb 3, 2026
6a4bf7a
Fix upgrade parameter syntax - must be quoted R expression
jeliason Feb 3, 2026
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1 change: 1 addition & 0 deletions .github/workflows/tests.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ jobs:

- uses: r-lib/actions/setup-r-dependencies@v2
with:
upgrade: 'TRUE'
extra-packages: |
any::testthat
any::devtools
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15 changes: 9 additions & 6 deletions R/sic_extraction.R
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Original file line number Diff line number Diff line change
Expand Up @@ -153,8 +153,9 @@ compute_sic_posterior <- function(fit,
for (group_i in indices) {
for (source in source_types) {
# Find coefficient indices for this target-source pair
coef_pattern <- paste0("_", target_type, "_", source)
coef_ix <- grep(coef_pattern, coef_names, fixed = TRUE)
# Use $ anchor to match exact source name at end (avoids matching cd4tcells_ICOS when looking for cd4tcells)
coef_pattern <- paste0("_", target_type, "_", source, "$")
coef_ix <- grep(coef_pattern, coef_names)

if (length(coef_ix) == 0) {
warning(sprintf("No coefficients found for %s -> %s", source, target_type))
Expand Down Expand Up @@ -221,8 +222,9 @@ compute_sic_posterior <- function(fit,
for (patient_i in indices) {
for (source in source_types) {
# Find coefficient indices for this target-source pair
coef_pattern <- paste0("_", target_type, "_", source)
coef_ix <- grep(coef_pattern, coef_names, fixed = TRUE)
# Use $ anchor to match exact source name at end (avoids matching cd4tcells_ICOS when looking for cd4tcells)
coef_pattern <- paste0("_", target_type, "_", source, "$")
coef_ix <- grep(coef_pattern, coef_names)

if (length(coef_ix) == 0) {
warning(sprintf("No coefficients found for %s -> %s", source, target_type))
Expand Down Expand Up @@ -283,8 +285,9 @@ compute_sic_posterior <- function(fit,
for (image_i in indices) {
for (source in source_types) {
# Find coefficient indices for this target-source pair
coef_pattern <- paste0("_", target_type, "_", source)
coef_ix <- grep(coef_pattern, coef_names, fixed = TRUE)
# Use $ anchor to match exact source name at end (avoids matching cd4tcells_ICOS when looking for cd4tcells)
coef_pattern <- paste0("_", target_type, "_", source, "$")
coef_ix <- grep(coef_pattern, coef_names)

if (length(coef_ix) == 0) {
warning(sprintf("No coefficients found for %s -> %s", source, target_type))
Expand Down