From 91942ed65ef8f0b884de847da01bdb1c8ef73101 Mon Sep 17 00:00:00 2001
From: marcjwilliams1 <marcjwilliams1@gmail.com>
Date: Tue, 24 Aug 2021 05:21:00 -0400
Subject: [PATCH] Add utility function for filtering cells)

---
 NAMESPACE |  1 +
 R/util.R  | 17 ++++++++++++++---
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index dae2e1c..8bcc629 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -25,6 +25,7 @@ export(createSNVmatrix)
 export(create_cntransitions)
 export(create_segments)
 export(createbreakpointmatrix)
+export(filterbycells)
 export(filtercn)
 export(fix_assignments)
 export(fixjitter)
diff --git a/R/util.R b/R/util.R
index 535f394..84eac1a 100644
--- a/R/util.R
+++ b/R/util.R
@@ -963,10 +963,10 @@ BAFdistance <- function(cn) {
 filtercn <- function(cn, 
                      average_distance_filt = 0.1, 
                      ploidy_filt = NULL, 
-                     totalcounts_filt = 0, 
+                     totalhapcounts_filt = 0, 
                      nsegments_filt = 0){
-  qcnew <- dplyr::filter(cn$qc_per_cell, average_distance >= average_distance_filt,
-                             totalcounts >= totalcounts_filt,
+  qcnew <- dplyr::filter(cn$qc_per_cell, average_distance <= average_distance_filt,
+                             totalhapcounts >= totalhapcounts_filt,
                               nsegments >= nsegments_filt)
   if (!is.null(ploidy_filt)){
     qcnew <- dplyr::filter(qcnew, ploidy == ploidy_filt)
@@ -980,3 +980,14 @@ filtercn <- function(cn,
   
   return(cn)
 }
+
+#' @export
+filterbycells <- function(cn, cells){
+  cn$data <- cn$data %>% 
+    dplyr::filter(cell_id %in% cells)
+  cn$qc_per_cell <- cn$qc_per_cell %>% 
+    dplyr::filter(cell_id %in% cells)
+  cn$qc_summary <- qc_summary(cn)
+  
+  return(cn)
+}