do not remove all rows when one under obs limit

mschubert · Nov 3, 2023 · 86eb76c · 86eb76c
1 parent 5e19eea
commit 86eb76c
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/genesets/test_fet.r b/genesets/test_fet.r
@@ -40,7 +40,7 @@ test_fet = function(valid, hits, sets, min=2, max=Inf) {
         setNames(names(sets)) %>%
         dplyr::bind_rows(.id="label") %>%
         as_tibble() %>%
-        na.omit() %>%
+        filter(size >= min) %>%
         select(label, size, size_used, everything()) %>%
         mutate(adj.p = p.adjust(p.value, method="fdr")) %>%
         arrange(adj.p, p.value)

diff --git a/genesets/test_lm.r b/genesets/test_lm.r
@@ -19,8 +19,9 @@ test_lm = function(genes, sets,
                    min_n=2, add_means=c(), trim=0, cl=0) {
     test_one = function(res, set) {
         dset = res %>% mutate(in_set = !! rlang::sym(label) %in% set + 0)
-        if (sum(dset$in_set, na.rm=TRUE) < min_n)
-            return(data.frame(estimate=NA, size=length(set), size_used=NA))
+        sz_use = sum(dset$in_set, na.rm=TRUE)
+        if (sz_use < min_n)
+            return(data.frame(size=length(set), size_used=sz_use))
 
         sums = dset %>% group_by(in_set) %>%
             summarize_at(vars(all_of(add_means)), function(x) mean(x, na.rm=TRUE, trim=trim)) %>%
@@ -70,7 +71,7 @@ test_lm = function(genes, sets,
         setNames(names(sets)) %>%
         dplyr::bind_rows(.id="label") %>%
         as_tibble() %>%
-        na.omit() %>%
+        filter(size_used >= min_n) %>%
         select(label, size, size_used, !!! rlang::syms(add_means), everything()) %>%
         mutate(adj.p = p.adjust(p.value, method="fdr")) %>%
         arrange(adj.p, p.value)