From 275bc2455b7211a58a68e4efe1b56f9cdffed0f9 Mon Sep 17 00:00:00 2001
From: rptashkin <r.ptashkin@gmail.com>
Date: Mon, 27 Jul 2020 15:19:23 -0400
Subject: [PATCH] impute sex from tumor sample when run in unmatched mode,
 experimental

---
 DESCRIPTION                     | 2 +-
 R/read-snp-matrix.R             | 7 ++++---
 man/read_snp_matrix_facets2n.Rd | 5 ++++-
 run-facets-wrapper.R            | 2 +-
 4 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 34db115..3949026 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -29,7 +29,7 @@ Imports:
     facets (>= 0.5.6), 
     facets2n (>= 0.2.6)
 NeedsCompilation: no
-Packaged: 2020-07-23 14:48:17 UTC; rptashkin
+Packaged: 2020-07-23 15:08:07 UTC; rptashkin
 Suggests: 
     covr (>= 3.2.0),
     testthat (>= 2.1.0)
diff --git a/R/read-snp-matrix.R b/R/read-snp-matrix.R
index 214383f..6d2dec1 100644
--- a/R/read-snp-matrix.R
+++ b/R/read-snp-matrix.R
@@ -45,7 +45,7 @@ read_snp_matrix = function(input_file,
 
 read_snp_matrix_facets2n = function(filename, err.thresh=Inf, del.thresh=Inf, perl.pileup=FALSE,
                                     MandUnormal=FALSE, spanT=0.2, spanA=0.2, spanX=0.2, gbuild="hg19",
-                                    ReferencePileupFile=NULL, ReferenceLoessFile=NULL, MinOverlap=0.9, useMatchedX=FALSE, refX=FALSE){
+                                    ReferencePileupFile=NULL, ReferenceLoessFile=NULL, MinOverlap=0.9, useMatchedX=FALSE, refX=FALSE, unmatched=FALSE){
     #' #' Read in the snp-pileup generated SNP read count matrix file for facets2n processing
     #' @importFrom utils read.csv
     #' @param filename counts file from snp-pileup
@@ -54,6 +54,7 @@ read_snp_matrix_facets2n = function(filename, err.thresh=Inf, del.thresh=Inf, pe
     #' @param del.thresh (numeric) Deletion threshold to be used to filter snp-pileup data frame.
     #' @param perl.pileup (logical) Is the pileup data generated using perl pileup tool?
     #' @param MandUnormal (logical) Is CNLR analysis to be peformed using unmatched reference normals?
+    #' @param unmatched (logical) is the tumor being analyzed unmatched
     #' @param spanT (numeric) Default span value to be used for loess normalization in tumor sample.
     #' @param spanA (numeric) Default span value to be used for loess normalization across autosomal chromosomes in the normal sample.
     #' @param spanX (numeric) Default span value to be used for loess normalization in Chr X in the normal sample.
@@ -69,8 +70,8 @@ read_snp_matrix_facets2n = function(filename, err.thresh=Inf, del.thresh=Inf, pe
     #' @importFrom pctGCdata getGCpct
     #' @export
     if (MandUnormal){
-        facets2n::readSnpMatrix(filename, MandUnormal = MandUnormal, ReferencePileupFile = ReferencePileupFile, ReferenceLoessFile = ReferenceLoessFile, useMatchedX = useMatchedX, refX = refX)
+        facets2n::readSnpMatrix(filename, MandUnormal = MandUnormal, ReferencePileupFile = ReferencePileupFile, ReferenceLoessFile = ReferenceLoessFile, useMatchedX = useMatchedX, refX = refX, unmatched=unmatched)
     }else{
-        facets2n::readSnpMatrix(filename, MandUnormal = MandUnormal)
+        facets2n::readSnpMatrix(filename, MandUnormal = MandUnormal, unmatched=unmatched)
     }
 }
diff --git a/man/read_snp_matrix_facets2n.Rd b/man/read_snp_matrix_facets2n.Rd
index b18eb6f..51b3e42 100644
--- a/man/read_snp_matrix_facets2n.Rd
+++ b/man/read_snp_matrix_facets2n.Rd
@@ -21,7 +21,8 @@ read_snp_matrix_facets2n(
   ReferenceLoessFile = NULL,
   MinOverlap = 0.9,
   useMatchedX = FALSE,
-  refX = FALSE
+  refX = FALSE,
+  unmatched = FALSE
 )
 }
 \arguments{
@@ -53,6 +54,8 @@ read_snp_matrix_facets2n(
 
 \item{refX}{(logical) Use sex matched reference normal for chrX normalization}
 
+\item{unmatched}{(logical) is the tumor being analyzed unmatched}
+
 \item{skip}{(character) Skip n number of lines in the input file.}
 }
 \value{
diff --git a/run-facets-wrapper.R b/run-facets-wrapper.R
index fe30a06..28a41da 100755
--- a/run-facets-wrapper.R
+++ b/run-facets-wrapper.R
@@ -223,7 +223,7 @@ if (dir.exists(directory)) {
 # Read SNP counts file
 message(paste('Reading', args$counts_file))
 if(args$facets2n_lib_path != ''){
-    read_counts = read_snp_matrix_facets2n(args$counts_file,MandUnormal= args$MandUnormal, ReferencePileupFile=args$reference_snp_pileup, ReferenceLoessFile=args$reference_loess_file, useMatchedX=args$useMatchedX, refX=args$refX)
+    read_counts = read_snp_matrix_facets2n(args$counts_file,MandUnormal= args$MandUnormal, ReferencePileupFile=args$reference_snp_pileup, ReferenceLoessFile=args$reference_loess_file, useMatchedX=args$useMatchedX, refX=args$refX, unmatched=args$unmatched)
 }else{
     read_counts = read_snp_matrix(args$counts_file)
 }