Revise examples to assign results to objects

rqtl · Jun 30, 2020 · 8e8c54b · 8e8c54b
1 parent 2818d07
commit 8e8c54b
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Showing 12 changed files with 10 additions and 16 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git a/man/count_unique_geno.Rd b/man/count_unique_geno.Rd
diff --git a/man/encode_geno.Rd b/man/encode_geno.Rd
diff --git a/man/find_consensus_geno.Rd b/man/find_consensus_geno.Rd
diff --git a/man/find_unique_geno.Rd b/man/find_unique_geno.Rd
diff --git a/man/scan_qtl_to_qtl2.Rd b/man/scan_qtl_to_qtl2.Rd