From 2137fe62fd2b234920d12e44f0b5075cc9af170d Mon Sep 17 00:00:00 2001
From: jalavery <laveryj@mskcc.org>
Date: Wed, 17 Jul 2024 11:27:21 -0400
Subject: [PATCH] documentation for summarize_by_patient

---
 NAMESPACE                   |  1 +
 man/summarize_by_patient.Rd | 40 +++++++++++++++++++++++++++++++++++++
 2 files changed, 41 insertions(+)
 create mode 100644 man/summarize_by_patient.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 64912381..03b10abe 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -32,6 +32,7 @@ export(specify_impact_panels)
 export(subset_by_frequency)
 export(subset_by_panel)
 export(summarize_by_gene)
+export(summarize_by_patient)
 export(tbl_genomic)
 export(which_impact_panel)
 import(ComplexHeatmap)
diff --git a/man/summarize_by_patient.Rd b/man/summarize_by_patient.Rd
new file mode 100644
index 00000000..b36e0303
--- /dev/null
+++ b/man/summarize_by_patient.Rd
@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/summarize-by-patient.R
+\name{summarize_by_patient}
+\alias{summarize_by_patient}
+\title{Simplify binary matrix to one column per patient that counts any alteration
+type across all samples as 1}
+\usage{
+summarize_by_patient(gene_binary, other_vars = NULL)
+}
+\arguments{
+\item{gene_binary}{a 0/1 matrix of gene alterations}
+
+\item{other_vars}{One or more column names (quoted or unquoted) in data to be retained
+in resulting data frame. Default is NULL.}
+}
+\value{
+a binary matrix with a row for each sample and one column per gene
+}
+\description{
+This will reduce the number of columns in your binary matrix, and the
+resulting data frame will have only 1 col per gene, as opposed to separate
+columns for mutation/cna/fusion.
+}
+\details{
+Note that if samples to the same patient were sequenced on different panels,
+any indication of an alteration is counted as an alteration, but the absence
+of an alteration is only defined when all sequencing panels included the gene
+and indicated that it was not altered.
+}
+\examples{
+samples <- unique(gnomeR::mutations$sampleId)[1:10]
+gene_binary <- create_gene_binary(
+  samples = samples, mutation = mutations, cna = cna,
+  mut_type = "somatic_only",
+  include_silent = FALSE,
+  specify_panel = "IMPACT341"
+) \%>\%
+  summarize_by_patient()
+
+}