Merge pull request #228 from PNNL-CompBio/dev

updated xcell to work with matrisome
PNNL-CompBio · Oct 13, 2023 · e524764 · e524764
2 parents bc33137 + 6560ad0
commit e524764
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Showing 6 changed files with 1 addition and 23,225 deletions.
diff --git a/toy_data/TOY_log2ratio_protein_abundance_withNA.csv b/toy_data/TOY_log2ratio_protein_abundance_withNA.csv
diff --git a/toy_data/TOY_log2ratio_protein_abundance_withNA.tsv b/toy_data/TOY_log2ratio_protein_abundance_withNA.tsv
diff --git a/toy_data/TOY_rna_expression_imputed.tsv b/toy_data/TOY_rna_expression_imputed.tsv
diff --git a/toy_data/TOY_rna_expression_withNA.tsv b/toy_data/TOY_rna_expression_withNA.tsv
diff --git a/toy_data/TOY_signature_matrix.tsv b/toy_data/TOY_signature_matrix.tsv
diff --git a/tumorDeconvAlgs/xcell/xcell.r b/tumorDeconvAlgs/xcell/xcell.r
@@ -40,7 +40,7 @@ if (length(args) > 1) {
         if (length(markers) == 0) {
             tempMarkers <- rownames(ref[ref[,s] > quantile(ref[,s], prob=0.5),])
             deOverMedians <- (ref[tempMarkers,s] - rowMedians(as.matrix(ref[tempMarkers,])))/rowMedians(as.matrix(ref[tempMarkers,]))
-            markers <- tempMarkers[deOverMedians > quantile(deOverMedians, prob=0.9)]
+            markers <- tempMarkers[deOverMedians >= quantile(deOverMedians, prob=0.9)]
         }
         marker[[i]] <- markers
         taggedNames <- c(taggedNames, paste0(colnames(ref)[i], "%", cellTypeNames[i], toString(i), "%", cellTypeNames[i], toString(i), ".txt"))