add readme

DESCRIPTION

@@ -3,11 +3,9 @@ Package: fastROGUE
 Title: Parallel version of ROGUE (Ratio of Global Unshifted Entropy)
 Version: 1.0
 Authors@R: c(
-  person("Pauling", "Liu", role = c("aut", "cre"),
-         email = "[email protected]"),
-  person("Zhiming", "Ye", role = c("ctb"),
-         email = "[email protected]")
-   )
+    person("Pauling", "Liu", , "[email protected]", role = c("aut", "cre")),
+    person("Zhiming", "Ye", , "[email protected]", role = "ctb")
+  )
 Description: An entropy-based universal metric for assessing the purity of
     single cell population with parallel calculation
 License: GPL (>=2)

R/ROGUE.R

@@ -299,7 +299,6 @@ ent.toli <- function(ent, expr, n = 2, span = 0.5, r = 1, mt.method = "fdr"){
 
 
 #' Calculate the ROGUE value of each putative cluster for each sample.
-#' @usage rogue(expr, labels, samples, platform = NULL, k= NULL, min.cell.n = 10, remove.outlier.n = 2, span = 0.5, r = 1, mt.method = c("fdr","BH"))
 #'
 #' @param expr The expression matrix. Rows should be genes and columns should be cells.
 #' @param labels A vector of cell cluster lables for all cells corresponding to 'expr' argument.

README.md

@@ -1,46 +1,92 @@
+# fastROGUE: A Parallelized Version of the Original ROGUE
+
+fastROGUE enables accelerated computation on complex data by utilizing parallel processing. The main update allows the rogue function to specify `ncores` for parallel computation.
+
+``` r
+rogue(
+  expr,
+  labels,
+  samples,
+  platform = NULL,
+  k = NULL,
+  min.cell.n = 10,
+  remove.outlier.n = 2,
+  span = 0.9,
+  r = 1,
+  filter = F,
+  min.cells = 10,
+  min.genes = 10,
+  mt.method = "fdr",
+  ncores = 4, # <--- This one! 
+  fix_to_numbers = T
+)
+```
+
+**Installing fastROGUE**\
+To install fastROGUE, run:
+
+```         
+if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
+devtools::install_github("ZhimingYe/fastROGUE")
+```
+
+------------------------------------------------------------------------
+
+Origin readme:
+
+------------------------------------------------------------------------
+
 # ROGUE (Ratio of Global Unshifted Entropy)
 
 ## Contents
 
-- [Overview](#overview)
-- [Installation Guide](#installation-guide)
-- [Tutorial](#tutorial)
-- [Reproduction instructions](#Reproduction-instructions)
-- [License](./LICENSE)
-- [Citation](#citation)
-- [Contact](#Contact)
+-   [Overview](#overview)
+-   [Installation Guide](#installation-guide)
+-   [Tutorial](#tutorial)
+-   [Reproduction instructions](#Reproduction-instructions)
+-   [License](./LICENSE)
+-   [Citation](#citation)
+-   [Contact](#Contact)
+
+## Overview {#overview}
 
-## Overview
 Often, it is not even clear whether a given cluster is uniform in unsupervised scRNA-seq data analyses. Here, we proposed the concept of cluster purity and introduced a conceptually novel statistic, named ROGUE, to examine whether a given cluster is a pure cell population.
 
-## Installation Guide
-**Installing dependency package**  
+## Installation Guide {#installation-guide}
+
+**Installing dependency package**\
 Before installing ROGUE, the “tidyverse” package should be installed first:
-```
+
+```         
 install.packages("tidyverse")
 ```
-**Installing ROGUE**  
+
+**Installing ROGUE**\
 To install ROGUE, run:
-```
+
+```         
 if (!requireNamespace("devtools", quietly = TRUE)) install.packages("devtools")
 devtools::install_github("PaulingLiu/ROGUE")
 ```
 
-## Tutorial
-For more details and basic usage see following tutorials:
-1.	[Guided Tutorial](https://htmlpreview.github.io/?https://github.com/PaulingLiu/ROGUE/blob/master/vignettes/ROGUE_Tutorials.html) (It takes a few seconds to load the HTML file)
+## Tutorial {#tutorial}
+
+For more details and basic usage see following tutorials: 1. [Guided Tutorial](https://htmlpreview.github.io/?https://github.com/PaulingLiu/ROGUE/blob/master/vignettes/ROGUE_Tutorials.html) (It takes a few seconds to load the HTML file)
+
+## Reproduction instructions {#reproduction-instructions}
 
-## Reproduction instructions
 The scripts for producing all the quantitative results in our manuscript can be found in [scripts](./scripts).
 
-## Citation
-If you use ROGUE in your research, please considering citing:
-- [Liu et al., Nature Communications 2020](https://www.nature.com/articles/s41467-020-16904-3)
+## Citation {#citation}
+
+If you use ROGUE in your research, please considering citing: - [Liu et al., Nature Communications 2020](https://www.nature.com/articles/s41467-020-16904-3)
 
-## Contact
-Please contact us:  
-Baolin Liu: [email protected]  
-Zemin Zhang: [email protected]
+## Contact {#contact}
+
+Please contact us:\
+Baolin Liu: [pauling.liu\@pku.edu.cn](mailto:[email protected]){.email}\
+Zemin Zhang: [zemin\@pku.edu.cn](mailto:[email protected]){.email}
 
 ## Copyright
+
 ©2019 Baolin Liu, Chenwei Li. [Zhang Lab](http://cancer-pku.cn/). All rights reserved.