From 6e8d047705de50d1ae46899698a201915da64c73 Mon Sep 17 00:00:00 2001
From: mbcole <mbeloc@gmail.com>
Date: Mon, 14 Nov 2016 16:18:36 -0800
Subject: [PATCH] Added example for factor sample filter

---
 R/sample_filtering.R        | 9 +++++++++
 man/factor_sample_filter.Rd | 9 +++++++++
 2 files changed, 18 insertions(+)

diff --git a/R/sample_filtering.R b/R/sample_filtering.R
index a9f5fa0..03e700b 100644
--- a/R/sample_filtering.R
+++ b/R/sample_filtering.R
@@ -426,6 +426,15 @@ metric_sample_filter = function(expr, nreads = colSums(expr), ralign = NULL,
 #' @importFrom diptest dip.test
 #' @import gplots
 #' @export
+#' 
+#' @examples
+#' mat <- matrix(rpois(1000, lambda = 5), ncol=10)
+#' colnames(mat) <- paste("X", 1:ncol(mat), sep="")
+#' qc = as.matrix(cbind(colSums(mat),colSums(mat > 0)))
+#' rownames(qc) = colnames(mat)
+#' colnames(qc) = c("NCOUNTS","NGENES")
+#' mfilt = factor_sample_filter(expr = mat,qc, plot = TRUE,qual_select_q_thresh = 1)
+#' 
 factor_sample_filter = function(expr, qual, gene_filter = NULL, max_exp_pcs = 5,
                                 qual_select_q_thresh = 0.01, force_metrics = NULL, good_metrics = NULL,
                                 min_qual_variance = 0.7, zcut = 1,
diff --git a/man/factor_sample_filter.Rd b/man/factor_sample_filter.Rd
index cbe93b9..1717d63 100644
--- a/man/factor_sample_filter.Rd
+++ b/man/factor_sample_filter.Rd
@@ -49,4 +49,13 @@ describing whether it passed filtering by factor-based filtering, using PCA of q
 \details{
 None
 }
+\examples{
+mat <- matrix(rpois(1000, lambda = 5), ncol=10)
+colnames(mat) <- paste("X", 1:ncol(mat), sep="")
+qc = as.matrix(cbind(colSums(mat),colSums(mat > 0)))
+rownames(qc) = colnames(mat)
+colnames(qc) = c("NCOUNTS","NGENES")
+mfilt = factor_sample_filter(expr = mat,qc, plot = TRUE,qual_select_q_thresh = 1)
+
+}