Revert "fixing #68"

This reverts commit e39fe5b.

NEWS.md

@@ -1,8 +1,8 @@
 # numbat 1.0.5 - 11/27/2022
 
-* Fixing bugs #65, #66, #67, #68
+* Fixing bugs #65, #66, #67
 
-* Retiring dependency on `reshape2`
+* Retire dependency on `reshape2`
 
 # numbat 1.0.4 - 11/20/2022
 

R/main.R

@@ -673,6 +673,7 @@ exp_hclust = function(count_mat, lambdas_ref, gtf, sc_refs = NULL, window = 101,
 #' @keywords internal 
 make_group_bulks = function(groups, count_mat, df_allele, lambdas_ref, gtf, min_depth = 0, ncores = NULL) {
 
+
     if (length(groups) == 0) {
         return(data.frame())
     }
@@ -1552,7 +1553,7 @@ get_joint_post = function(exp_post, allele_post, segs_consensus) {
 #' @keywords internal 
 retest_bulks = function(bulks, segs_consensus = NULL,
     t = 1e-5, min_genes = 10, gamma = 20, 
-    use_loh = FALSE, diploid_chroms = NULL, ncores = 1, exclude_neu = TRUE, min_LLR = 5) {
+    segs_loh = NULL, use_loh = FALSE, diploid_chroms = NULL, ncores = 1, exclude_neu = TRUE, min_LLR = 5) {
 
     if (is.null(segs_consensus)) {
         segs_consensus = get_segs_consensus(bulks)

R/utils.R

@@ -507,7 +507,7 @@ analyze_bulk = function(
         stop('Must define diploid region if not given')
     }
 
-    if (is.null(segs_loh) & (!'loh' %in% colnames(bulk))) {
+    if (is.null(segs_loh)) {
         bulk = bulk %>% mutate(loh = FALSE)
     }
 
@@ -584,10 +584,6 @@ analyze_bulk = function(
                 cnv_state_post = ifelse(is.na(cnv_state_post), 'neu', cnv_state_post),
                 cnv_state = ifelse(is.na(cnv_state), 'neu', cnv_state)
             ) %>%
-            mutate(
-                cnv_state_post = ifelse(loh, 'del', cnv_state_post),
-                cnv_state = ifelse(loh, 'del', cnv_state)
-            ) %>%
             mutate(state_post = ifelse(
                 cnv_state_post %in% c('amp', 'del', 'loh') & (!cnv_state %in% c('bamp', 'bdel')),
                 paste0(cnv_state_post, '_', str_extract(state, 'up_1|down_1|up_2|down_2|up|down|1_up|2_up|1_down|2_down')),