From 7badae96a5406997f756c7d0024d512c33218951 Mon Sep 17 00:00:00 2001
From: Schultheis <hschult@kerckhoff.mpg.de>
Date: Fri, 8 Mar 2019 15:35:06 +0100
Subject: [PATCH] tobias_parser: added details

---
 R/parser.R           | 5 +++++
 man/tobias_parser.Rd | 7 ++++++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/R/parser.R b/R/parser.R
index 195b11c..13591b8 100644
--- a/R/parser.R
+++ b/R/parser.R
@@ -381,6 +381,8 @@ parser <- function(file, dec = ".") {
 
 #' TOBIAS TFBS table to clarion parser
 #'
+#' Click \href{https://github.molgen.mpg.de/loosolab/TOBIAS}{here} for more information about TOBIAS.
+#'
 #' @param input Path to input table
 #' @param output Output path.
 #' @param filter_columns Either a vector of columnnames or a file containing one columnname per row.
@@ -393,6 +395,9 @@ parser <- function(file, dec = ".") {
 #' @param dec Decimal separator. Used in file reading and writing.
 #' @param ... Used as header information.
 #'
+#' @details During conversion the parser will try to use the given config (if provided) to create the \href{https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format}{Clarion} metadata. In the case of insufficient config information it will try to approximate by referencing condition names issuing warnings in the process.
+#' @details Factor grouping (metadata factor columns) is currently not implemented!
+#'
 #' @export
 tobias_parser <- function(input, output, filter_columns = NULL, filter_pattern = NULL, config = system.file("extdata", "tobias_config.json", package = "wilson"), omit_NA = FALSE, condition_names = NULL, condition_pattern = "_bound$", in_field_delimiter = ",", dec = ".", ...) {
   ## filter data columns
diff --git a/man/tobias_parser.Rd b/man/tobias_parser.Rd
index 576be38..0606214 100644
--- a/man/tobias_parser.Rd
+++ b/man/tobias_parser.Rd
@@ -34,5 +34,10 @@ tobias_parser(input, output, filter_columns = NULL,
 \item{...}{Used as header information.}
 }
 \description{
-TOBIAS TFBS table to clarion parser
+Click \href{https://github.molgen.mpg.de/loosolab/TOBIAS}{here} for more information about TOBIAS.
+}
+\details{
+During conversion the parser will try to use the given config (if provided) to create the \href{https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format}{Clarion} metadata. In the case of insufficient config information it will try to approximate by referencing condition names issuing warnings in the process.
+
+Factor grouping (metadata factor columns) is currently not implemented!
 }