chore: update Roxygen doc and Rd files

markgene · Apr 6, 2018 · 4939dbf · 4939dbf
1 parent 53079c5
commit 4939dbf
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Showing 11 changed files with 7 additions and 118 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: maxprobes
 Type: Package
 Title: Methylation Array Cross-Reactive Probes
-Version: 0.0.1
+Version: 0.0.2
 Authors@R: c(
     person("Mark", "Chen", email = "mjchen.gene@gmail.com", role = "cre"))
 Maintainer: Mark J Chen <mjchen.gene@gmail.com>

diff --git a/R/cross-reactive.R b/R/cross-reactive.R
@@ -69,6 +69,7 @@ dropXreactiveLoci <- function(x) {
 #' \href{https://github.com/sirselim/illumina450k_filtering}{GitHub: sirselim/illumina450k_filtering}.
 #'
 #' @return A character vector of probe IDs
+#' @noRd
 read_xreactive_probes_450k_chen <- function() {
   infile <- system.file("extdata", "48639-non-specific-probes-Illumina450k.csv", package = "sjma")
   xreactive_probes <- read.csv(infile, stringsAsFactors = FALSE)
@@ -87,6 +88,7 @@ read_xreactive_probes_450k_chen <- function() {
 #' \href{https://github.com/sirselim/illumina450k_filtering}{GitHub: sirselim/illumina450k_filtering}.
 #'
 #' @return A character vector of probe IDs
+#' @noRd
 read_xreactive_probes_450k_benton <- function() {
   infile <- system.file("extdata", "HumanMethylation450_15017482_v.1.1_hg19_bowtie_multimap.txt", package = "sjma")
   xreactive_probes <- read.csv(infile, stringsAsFactors = FALSE, header = FALSE)
@@ -106,6 +108,7 @@ read_xreactive_probes_450k_benton <- function() {
 #' \href{https://github.com/sirselim/illumina450k_filtering}{GitHub: sirselim/illumina450k_filtering}.
 #'
 #' @return A character vector of probe IDs
+#' @noRd
 read_xreactive_probes_epic_pidsley <- function() {
   infile <- system.file("extdata", "13059_2016_1066_MOESM1_ESM.csv", package = "sjma")
   xreactive_probes <- read.csv(infile, stringsAsFactors = FALSE, header = TRUE)
@@ -122,6 +125,7 @@ read_xreactive_probes_epic_pidsley <- function() {
 #' The cross-reactive probes are downloaded from Table S2 and S3.
 #'
 #' @return A character vector of probe IDs
+#' @noRd
 read_xreactive_probes_epic_mccartney <- function() {
   s2_file <- system.file("extdata", "1-s2.0-S221359601630071X-mmc2.txt", package = "sjma")
   s3_file <- system.file("extdata", "1-s2.0-S221359601630071X-mmc3.txt", package = "sjma")

diff --git a/R/data.R b/R/data.R
@@ -3,6 +3,7 @@
 #' Generate internal data available to package functions.
 #'
 #' @return NULL
+#' @noRd
 generate_internal_data <- function() {
   # Cross-reactive probes 450K
   xreactive_probes_450k_chen <- read_xreactive_probes_450k_chen()

diff --git a/R/helpers.R b/R/helpers.R
@@ -5,6 +5,7 @@
 #'
 #' @param x An object containing annotation information
 #' @return A character scale of either "EPIC" or "450K"
+#' @noRd
 get_array_type <- function(x) {
   anno_info <- annotation(x)
   if (anno_info["array"] == "IlluminaHumanMethylationEPIC") {

diff --git a/man/generate_internal_data.Rd b/man/generate_internal_data.Rd
diff --git a/man/get_array_type.Rd b/man/get_array_type.Rd
diff --git a/man/hello.Rd b/man/hello.Rd
diff --git a/man/read_xreactive_probes_450k_benton.Rd b/man/read_xreactive_probes_450k_benton.Rd
diff --git a/man/read_xreactive_probes_450k_chen.Rd b/man/read_xreactive_probes_450k_chen.Rd
diff --git a/man/read_xreactive_probes_epic_mccartney.Rd b/man/read_xreactive_probes_epic_mccartney.Rd
diff --git a/man/read_xreactive_probes_epic_pidsley.Rd b/man/read_xreactive_probes_epic_pidsley.Rd