📖 DOC: update

Author: ShixiangWang

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: UCSCXenaTools
 Title: Download and Explore Datasets from UCSC Xena Data Hubs
-Version: 1.2.0
+Version: 1.2.0.9000
 Authors@R: c(person("Shixiang", "Wang", email = "w_shixiang@163.com", role = c("aut", "cre"), 
             comment = c(ORCID = "0000-0001-9855-7357")),
             person("Martin", "Morgan", role="aut"))

NAMESPACE

@@ -20,6 +20,7 @@ export(samples)
 export(showTCGA)
 export(to_snake)
 export(xena_default_hosts)
+exportClasses(XenaHub)
 import(dplyr)
 import(methods)
 import(shiny)
@@ -28,6 +29,7 @@ importFrom(httr,POST)
 importFrom(httr,content)
 importFrom(httr,stop_for_status)
 importFrom(magrittr,"%>%")
+importFrom(methods,new)
 importFrom(readr,cols)
 importFrom(readr,read_tsv)
 importFrom(readr,read_tsv_chunked)

NEWS.md

@@ -1,18 +1,26 @@
-# UCSCXenaTools 
+# v1.2.1
 
-## v1.2.0
+## Bug fixes
+
+* fix API functions cannot be called from outside
+
+## Minor changes
+
+* export `XenaHub` Class
+
+# v1.2.0
 
 * reformat code files
 * update `XenaData` & `XenaDataUpdate()` function to obtain more info
 * add `jsonlite` as import package
 * add metadata for all datasets into package `inst` dir
 
-## v1.1.1
+# v1.1.1
 
 * update doc for APIs 
 * modify description for package
 
-## v1.1.0
+# v1.1.0
 
 * this version will change many variable names or functions. Update and Read the [documentation](https://github.com/ShixiangWang/UCSCXenaTools) are highly recommended!
 * add API functions, this is inspired by [xenaPython](https://github.com/ucscXena/xenaPython) package
@@ -22,47 +30,47 @@
 * new `XenaData` contains much more information
 * improve internal code
 
-## v1.0.1
+# v1.0.1
 
 * fix some grammar errors in documentation
 
-## v1.0.0
+# v1.0.0
 
 * update README, documentation and vignette
 * fix some typo
 * new function: `XenaBrowse` - open the dataset link using web browser
 * open grel all parameters to `XenaFilter` function
 
-## v0.2.7
+# v0.2.7
 
 * fix bug #2
 * add pipe operator
 * add doc & docs
 
-## v0.2.6
+# v0.2.6
 
 * add new datahub [**ATACseq**](https://xenabrowser.net/datapages/?host=https%3A%2F%2Fatacseq.xenahubs.net&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443) 
 * enhance preparing data to R: provide options to select subset of original file data (see #1)
 
-## v0.2.5
+# v0.2.5
 
 * add new datahub **PCAWG**
 * speed up `XenaFilter` function
 
-## v0.2.4
+# v0.2.4
 
 * add new function `getTCGAdata` to help user download TCGA data by projects and biological data type
 
-## v0.2.3
+# v0.2.3
 
 * add shiny app to show TCGA datasets information of Xena
 * add `downloadTCGA` function to help user quickly download TCGA datasets
 
-## v0.2.2
+# v0.2.2
 
 * fix question about using temp directory
 
-## v0.2.1
+# v0.2.1
 
 * Add two hosts: Treehouse and TCGA Pan-Cancer
 

R/XenaHub-class.R

@@ -1,10 +1,12 @@
 #FUN: Set Class & operate XenaHub object directly
 
-##'  @title a S4 class to represent UCSC Xena Data Hubs
-##'  @slot hosts hosts of data hubs
-##'  @slot cohorts cohorts of data hubs
-##'  @slot datasets datasets of data hubs
-##'  @importFrom methods new
+##' Class XenaHub
+##' @description  a S4 class to represent UCSC Xena Data Hubs
+##' @slot hosts hosts of data hubs
+##' @slot cohorts cohorts of data hubs
+##' @slot datasets datasets of data hubs
+##' @importFrom methods new
+##' @export
 .XenaHub = setClass(
     "XenaHub",
     representation = representation(