making it more robust in cases of not perfectly overlapping samples

PNNL-Comp-Mass-Spec · May 11, 2024 · e1a324c · e1a324c
1 parent 3a51d2a
commit e1a324c
Showing 1 changed file with 7 additions and 0 deletions.
diff --git a/R/ptm_adjustment_by_global.R b/R/ptm_adjustment_by_global.R
@@ -21,6 +21,13 @@
 
 adjust_for_parent_protein_profiles <- function(m_ptm, m_global){
 
+   # sample alignment
+   common_samples <- intersect(sampleNames(m_ptm), sampleNames(m_global))
+   stopifnot(length(common_saples) < 2)
+   m_ptm <- m_ptm[,common_samples]
+   m_global <- m_global[,common_samples]
+
+   # gene matching
    stopifnot("Gene" %in% fvarLabels(m_ptm))
 
    gene_overlap <- intersect(fData(m_ptm)$Gene, featureNames(m_global))