From 567db9cc162fa6710d36a717abc005cfb9a00630 Mon Sep 17 00:00:00 2001
From: David Young <david@textflex.com>
Date: Thu, 9 Jun 2022 15:02:43 +0800
Subject: [PATCH 1/2] Fix proportion estimation for NA values

Skip NA common genes from the bulk sample by recording indices where NA common genes are found and removing the corresponding column names from the output.
---
 R/Deconvolution.R | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/R/Deconvolution.R b/R/Deconvolution.R
index b86d59d..ec9770c 100644
--- a/R/Deconvolution.R
+++ b/R/Deconvolution.R
@@ -597,12 +597,19 @@ SCDC_prop <- function (bulk.eset, sc.eset, ct.varname, sample, ct.sub, iter.max
     prop.est.mvw <- NULL
     yhat <- NULL
     yhatgene.temp <- rownames(basis.mvw)
+    to.remove <- list()
     for (i in 1:N.bulk) {
       basis.mvw.temp <- basis.mvw
       xbulk.temp <- xbulk[, i]*100
       sigma.temp <- sigma
+      com.genes <- sum(xbulk[, i] != 0)
       message(paste(colnames(xbulk)[i], "has common genes",
-                    sum(xbulk[, i] != 0), "..."))
+                    com.genes, "..."))
+      if (is.na(com.genes)) {
+        # store indices of NA vals to remove later
+        to.remove <- append(to.remove, -i)
+        next
+      }
       lm <- nnls::nnls(A = basis.mvw.temp, b = xbulk.temp)
       delta <- lm$residuals
       wt.gene <- 1/(nu + delta^2 + colSums((lm$x * ALS.S)^2 *
@@ -640,9 +647,13 @@ SCDC_prop <- function (bulk.eset, sc.eset, ct.varname, sample, ct.sub, iter.max
       ])
     }
     colnames(prop.est.mvw) <- colnames(basis.mvw)
-    rownames(prop.est.mvw) <- colnames(xbulk)
-    colnames(yhat) <- colnames(xbulk)
+    # remove column names for NA vals
+    to.remove <- unlist(to.remove)
+    xbulk.cols <- colnames(xbulk)[to.remove]
+    rownames(prop.est.mvw) <- xbulk.cols
+    colnames(yhat) <- xbulk.cols
     yobs <- exprs(bulk.eset)
+    yobs <- yobs[, to.remove]
     yeval <- SCDC_yeval(y = yobs, yest = yhat, yest.names = c("SCDC"))
     peval <- NULL
     if (!is.null(truep)) {

From 4793fc9ffba44e318dfb79ff6979a019b90b7cd6 Mon Sep 17 00:00:00 2001
From: David Young <david@textflex.com>
Date: Thu, 14 Jul 2022 13:34:38 +0800
Subject: [PATCH 2/2] Fix attempting to remove NAs when none are present

Only remove indices if they exist, which avoids attempting to index by NULL and removing all `yobs` values.
---
 R/Deconvolution.R | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/R/Deconvolution.R b/R/Deconvolution.R
index ec9770c..dbf4e96 100644
--- a/R/Deconvolution.R
+++ b/R/Deconvolution.R
@@ -647,13 +647,17 @@ SCDC_prop <- function (bulk.eset, sc.eset, ct.varname, sample, ct.sub, iter.max
       ])
     }
     colnames(prop.est.mvw) <- colnames(basis.mvw)
+    
     # remove column names for NA vals
+    xbulk.cols <- colnames(xbulk)
+    yobs <- exprs(bulk.eset)
     to.remove <- unlist(to.remove)
-    xbulk.cols <- colnames(xbulk)[to.remove]
+    if (!is.null(to.remove)) {
+      xbulk.cols <- xbulk.cols[to.remove]
+      yobs <- yobs[, to.remove]
+    }
     rownames(prop.est.mvw) <- xbulk.cols
     colnames(yhat) <- xbulk.cols
-    yobs <- exprs(bulk.eset)
-    yobs <- yobs[, to.remove]
     yeval <- SCDC_yeval(y = yobs, yest = yhat, yest.names = c("SCDC"))
     peval <- NULL
     if (!is.null(truep)) {