Remove github notes and small updates

R/subset-by-frequency.R

@@ -51,7 +51,7 @@ subset_by_frequency <- function(gene_binary, t = .1, other_vars = NULL) {
 
   # Remove all NA columns ----------------------------------------------
   all_na_alt <- apply(alt_only,  2, function(x) {
-    sum(is.na(x)) == nrow(alt_only)
+    # sum(is.na(x)) == nrow(alt_only)
   })
 
   all_non_na_alt <- names(all_na_alt[!all_na_alt])

R/summarize-by-gene.R

@@ -52,16 +52,10 @@ summarize_by_gene <- function(gene_binary, other_vars = NULL) {
     select("sample_id") %>%
     mutate(sample_index = paste0("samp", 1:nrow(gene_binary)))
 
-<<<<<<< Updated upstream
-  alt_only <- as.matrix(select(gene_binary, -"sample_id"))
-  rownames(alt_only) <- sample_index$sample_index
-=======
-  # data frame of only alterations
-  alt_only <- select(gene_binary, -"sample_id", -any_of(other_vars)) %>%
-    as.matrix()
 
+  # data frame of only alterations
+  alt_only <- as.data.frame(select(gene_binary, -"sample_id", -any_of(other_vars)))
   row.names(alt_only) <- sample_index$sample_index
->>>>>>> Stashed changes
 
   # check numeric class ---------
   is_numeric <- apply(alt_only, 2, is.numeric)
@@ -106,13 +100,12 @@ summarize_by_gene <- function(gene_binary, other_vars = NULL) {
   # join back to sample ID and other vars
   simp_gene_binary <- all_bin %>%
     left_join(sample_index, ., by = "sample_index") %>%
-    select(-c("sample_index")) %>%
-    as.data.frame()%>%
-    left_join(gene_binary %>%
-                select(any_of(c("sample_id", other_vars))))%>%
-    suppressMessages()
+    select(-c("sample_index"))
+
+  simp_gene_binary <- simp_gene_binary %>%
+    left_join(select(gene_binary, any_of(c("sample_id", other_vars))), by = "sample_id")
 
-  simp_gene_binary
+  return(simp_gene_binary)
 
 }
 

tests/testthat/test-summarize-by-gene.R

@@ -106,18 +106,18 @@ test_that("test what happens to columns with all NA", {
 
   })
 
-<<<<<<< Updated upstream
-=======
+
 # test_that("all columns must be numeric to continue", {
 #
 # })
 
 test_that("other vars are retained", {
-  samples <- Reduce(intersect, list(gnomeR::mutations$sampleId, gnomeR::cna$sampleId,
+  samples <- Reduce(intersect, list(gnomeR::mutations$sampleId,
+                                    gnomeR::cna$sampleId,
                                     gnomeR::sv$sampleId))
 
 
-  bin_impact <- create_gene_binary(samples=samples,
+  bin_impact <- create_gene_binary(samples = samples,
                                     mutation = gnomeR::mutations,
                                     cna = gnomeR::cna,
                                     fusion = gnomeR::sv,
@@ -126,15 +126,16 @@ test_that("other vars are retained", {
 
   set.seed(20230828)
 
-  bin_impact$random_color = sample(c("blue", "red",
-                                     "yellow"), size = 50, replace = TRUE)
+  bin_impact$random_color = sample(c("blue", "red", "yellow"),
+                                   size = 50, replace = TRUE)
 
   expect_true("random_color" %in% names(bin_impact))
   sum_impact <- summarize_by_gene(bin_impact,
                                   other_vars = "random_color")
 
   expect_true("random_color" %in% names(sum_impact))
   expect_true("blue" %in% sum_impact$random_color)
->>>>>>> Stashed changes
+})
+