From 8e8c54be522dca80f6f925636bd2b8be10757518 Mon Sep 17 00:00:00 2001
From: Karl Broman <kbroman@gmail.com>
Date: Tue, 30 Jun 2020 06:52:16 -0500
Subject: [PATCH] Revise examples to assign results to objects

---
 R/cbind_smother.R          | 2 +-
 R/count_unique_geno.R      | 2 +-
 R/encode_geno.R            | 2 +-
 R/find_consensus_geno.R    | 2 +-
 R/find_unique_geno.R       | 2 +-
 R/scan_qtl_to_qtl2.R       | 3 ---
 man/cbind_smother.Rd       | 2 +-
 man/count_unique_geno.Rd   | 2 +-
 man/encode_geno.Rd         | 2 +-
 man/find_consensus_geno.Rd | 2 +-
 man/find_unique_geno.Rd    | 2 +-
 man/scan_qtl_to_qtl2.Rd    | 3 ---
 12 files changed, 10 insertions(+), 16 deletions(-)

diff --git a/R/cbind_smother.R b/R/cbind_smother.R
index 2bf7d2d..27049ae 100644
--- a/R/cbind_smother.R
+++ b/R/cbind_smother.R
@@ -19,7 +19,7 @@
 #' @examples
 #' df1 <- data.frame(x=c(1,2,3,NA,4), y=c(5,8,9,10,11), row.names=c("A", "B", "C", "D", "E"))
 #' df2 <- data.frame(z=c(7,8,0,9,10), y=c(6,NA,NA,9,10), row.names=c("A", "B", "F", "C", "D"))
-#' cbind_smother(df1, df2)
+#' df1n2 <- cbind_smother(df1, df2)
 cbind_smother <-
   function(mat1, mat2)
 {
diff --git a/R/count_unique_geno.R b/R/count_unique_geno.R
index 265bd94..d91dae5 100644
--- a/R/count_unique_geno.R
+++ b/R/count_unique_geno.R
@@ -23,7 +23,7 @@
 #'            c("NA", "NA", "NA", "A", "A"),
 #'            c("A",  "A",  "T",  "G", "G"),
 #'            c("C", "C",  "G",  "G", "NA"))
-#' count_unique_geno(g)
+#' counts <- count_unique_geno(g)
 count_unique_geno <-
 function(genotypes, na.strings=c("N", "H", "NA", ""), cores=1)
 {
diff --git a/R/encode_geno.R b/R/encode_geno.R
index 84c92cf..05e2d4a 100644
--- a/R/encode_geno.R
+++ b/R/encode_geno.R
@@ -23,7 +23,7 @@
 #'               c("A", "A", "AT", "TA", "TT"),
 #'               c("T", "G", NA,   "GT", "TT"))
 #' codes <- rbind(c("C", "G"), c("A", "T"), c("T", "G"))
-#' encode_geno(geno, codes)
+#' geno_encoded <- encode_geno(geno, codes)
 #'
 encode_geno <-
 function(geno, allele_codes, output_codes=c("-", "A", "H", "B"), cores=1)
diff --git a/R/find_consensus_geno.R b/R/find_consensus_geno.R
index a064f93..39fbda2 100644
--- a/R/find_consensus_geno.R
+++ b/R/find_consensus_geno.R
@@ -24,7 +24,7 @@
 #'            c("C",  "C", "G", "G", "A", NA,  NA, NA),
 #'            rep(NA, 8),
 #'            c("C", "C", "G", "G", "G", "C", "G", "G"))
-#' find_consensus_geno(g)
+#' consensus <- find_consensus_geno(g)
 find_consensus_geno <-
 function(genotypes, na.strings=c("N", "H", "NA", ""), cores=1)
 {
diff --git a/R/find_unique_geno.R b/R/find_unique_geno.R
index d9c7354..3cd4733 100644
--- a/R/find_unique_geno.R
+++ b/R/find_unique_geno.R
@@ -26,7 +26,7 @@
 #'            c("NA", "NA", "NA", "A", "A"),
 #'            c("A",  "A",  "T",  "G", "G"),
 #'            c("C", "C",  "G",  "G", "NA"))
-#' find_unique_geno(g)
+#' ug <- find_unique_geno(g)
 find_unique_geno <-
 function(genotypes, na.strings=c("N", "H", "NA", ""), cores=1)
 {
diff --git a/R/scan_qtl_to_qtl2.R b/R/scan_qtl_to_qtl2.R
index c988f4f..7c1b639 100644
--- a/R/scan_qtl_to_qtl2.R
+++ b/R/scan_qtl_to_qtl2.R
@@ -15,9 +15,6 @@
 #' out <- scanone(hyper)
 #' out2 <- scan_qtl_to_qtl2(out)
 #'
-#' library(qtl2)
-#' plot(out2$scan1, out2$map)
-#'
 #' @seealso [scan_qtl_to_qtl2()]
 #'
 #' @export
diff --git a/man/cbind_smother.Rd b/man/cbind_smother.Rd
index c0e93f8..d1772d3 100644
--- a/man/cbind_smother.Rd
+++ b/man/cbind_smother.Rd
@@ -26,5 +26,5 @@ in its place.
 \examples{
 df1 <- data.frame(x=c(1,2,3,NA,4), y=c(5,8,9,10,11), row.names=c("A", "B", "C", "D", "E"))
 df2 <- data.frame(z=c(7,8,0,9,10), y=c(6,NA,NA,9,10), row.names=c("A", "B", "F", "C", "D"))
-cbind_smother(df1, df2)
+df1n2 <- cbind_smother(df1, df2)
 }
diff --git a/man/count_unique_geno.Rd b/man/count_unique_geno.Rd
index aed1062..40b62c4 100644
--- a/man/count_unique_geno.Rd
+++ b/man/count_unique_geno.Rd
@@ -28,7 +28,7 @@ g <- rbind(c("NA", "A",  "A",  "A", "T"),
            c("NA", "NA", "NA", "A", "A"),
            c("A",  "A",  "T",  "G", "G"),
            c("C", "C",  "G",  "G", "NA"))
-count_unique_geno(g)
+counts <- count_unique_geno(g)
 }
 \seealso{
 \code{\link[=find_unique_geno]{find_unique_geno()}}
diff --git a/man/encode_geno.Rd b/man/encode_geno.Rd
index d6b55ae..09b71bb 100644
--- a/man/encode_geno.Rd
+++ b/man/encode_geno.Rd
@@ -34,7 +34,7 @@ geno <- rbind(c("C", "G", "C",  "GG", "CG"),
               c("A", "A", "AT", "TA", "TT"),
               c("T", "G", NA,   "GT", "TT"))
 codes <- rbind(c("C", "G"), c("A", "T"), c("T", "G"))
-encode_geno(geno, codes)
+geno_encoded <- encode_geno(geno, codes)
 
 }
 \seealso{
diff --git a/man/find_consensus_geno.Rd b/man/find_consensus_geno.Rd
index 2be61da..9d39247 100644
--- a/man/find_consensus_geno.Rd
+++ b/man/find_consensus_geno.Rd
@@ -29,7 +29,7 @@ g <- rbind(c("NA", "N", "A", "A", "T", "G", NA, "H"),
            c("C",  "C", "G", "G", "A", NA,  NA, NA),
            rep(NA, 8),
            c("C", "C", "G", "G", "G", "C", "G", "G"))
-find_consensus_geno(g)
+consensus <- find_consensus_geno(g)
 }
 \seealso{
 \code{\link[=find_unique_geno]{find_unique_geno()}}, \code{\link[=encode_geno]{encode_geno()}}
diff --git a/man/find_unique_geno.Rd b/man/find_unique_geno.Rd
index 43a1916..601af62 100644
--- a/man/find_unique_geno.Rd
+++ b/man/find_unique_geno.Rd
@@ -31,7 +31,7 @@ g <- rbind(c("NA", "A",  "A",  "A", "T"),
            c("NA", "NA", "NA", "A", "A"),
            c("A",  "A",  "T",  "G", "G"),
            c("C", "C",  "G",  "G", "NA"))
-find_unique_geno(g)
+ug <- find_unique_geno(g)
 }
 \seealso{
 \code{\link[=count_unique_geno]{count_unique_geno()}}, \code{\link[=encode_geno]{encode_geno()}}
diff --git a/man/scan_qtl_to_qtl2.Rd b/man/scan_qtl_to_qtl2.Rd
index 258b3dc..e6fc9d5 100644
--- a/man/scan_qtl_to_qtl2.Rd
+++ b/man/scan_qtl_to_qtl2.Rd
@@ -24,9 +24,6 @@ hyper <- calc.genoprob(hyper, step=1, error.prob=0.002)
 out <- scanone(hyper)
 out2 <- scan_qtl_to_qtl2(out)
 
-library(qtl2)
-plot(out2$scan1, out2$map)
-
 }
 \seealso{
 \code{\link[=scan_qtl_to_qtl2]{scan_qtl_to_qtl2()}}