added scCNA class

Author: darlanminussi

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2019
+COPYRIGHT HOLDER: CopyKit

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2019 CopyKit
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -1,2 +1,5 @@
-# Generated by roxygen2: fake comment so roxygen2 overwrites silently.
-exportPattern("^[^\\.]")
+# Generated by roxygen2: do not edit by hand
+
+export("%>%")
+export(readCNAVarbin)
+importFrom(magrittr,"%>%")

R/AllClasses.R

@@ -0,0 +1,19 @@
+### all clases for the copykit package
+
+###################################################################
+# defining scCNA class
+#'
+#'  @export
+#'  @import methods
+#'  @importClassesFrom SummarizedExperiment RangedSummarizedExperiment SingleCellExperiment
+#'  @importClassesFrom S4Vectors DataFrame SimpleList
+#'
+#'
+
+.scCNA <- setClass("scCNA", contains = "SingleCellExperiment")
+
+scCNA <- function(segment_ratios, ...) {
+  cna <-
+    SingleCellExperiment::SingleCellExperiment(list(segment_ratios = segment_ratios), ...)
+  .scCNA(cna)
+}

R/readCNAVarbin.R

@@ -0,0 +1,28 @@
+#' Load data from Copy Number Experiment
+#'
+#' Creates an S4 class scCNA from the output directory of the copy number pipeline.
+#'
+#' @param dir A path for the output of the copy number pipeline.
+#'
+#' @return A S4 class object containing the segment ratios for each bin (rows) and each sample (columns).
+#' @export
+#'
+#' @examples
+readCNAVarbin <- function(dir) {
+  # Reads a copy number directory and produces
+  # a scCNA object as output
+
+  seg_data <- readr::read_tsv(fs::dir_ls(
+    path = dir,
+    recurse = T,
+    glob = "*uber*seg.txt"
+  )) %>%
+    janitor::clean_names() %>%
+    dplyr::select(-c(chrom,
+                     chrompos,
+                     abspos)) %>%
+    as.data.frame()
+
+  cna_obj <- scCNA(list(segment_ratios = seg_data))
+
+}

R/utils-pipe.R

@@ -0,0 +1,11 @@
+#' Pipe operator
+#'
+#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
+#'
+#' @name %>%
+#' @rdname pipe
+#' @keywords internal
+#' @export
+#' @importFrom magrittr %>%
+#' @usage lhs \%>\% rhs
+NULL

README.Rmd

@@ -0,0 +1,39 @@
+---
+output: github_document
+---
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+# CopyKit
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of copykit is to provide a toolkit for the analysis of single-cell copy number data
+
+## Installation
+
+You can install the development version of CopyKit from github with:
+
+``` r
+devtools::install_github()
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+```{r example}
+# library(copykit)
+## basic example code
+```
+
+

README.md

@@ -0,0 +1,28 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# CopyKit
+
+<!-- badges: start -->
+
+<!-- badges: end -->
+
+The goal of copykit is to provide a toolkit for the analysis of
+single-cell copy number data
+
+## Installation
+
+You can install the development version of CopyKit from github with:
+
+``` r
+devtools::install_github()
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+# library(copykit)
+## basic example code
+```

inst/WORDLIST

@@ -0,0 +1,2 @@
+CopyKit
+github

man/pipe.Rd

@@ -0,0 +1,3 @@
+if(requireNamespace('spelling', quietly = TRUE))
+  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                             skip_on_cran = TRUE)

man/readCNAVarbin.Rd

@@ -0,0 +1,4 @@
+library(testthat)
+library(copykit)
+
+test_check("copykit")