Initial commit

.Rbuildignore

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+^MIPr\.Rproj$
+^\.Rproj\.user$
+^README\.Rmd$
+^LICENSE\.md$

.gitignore

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+.Rproj.user
+.Rhistory
+.Rdata
+.httr-oauth
+.DS_Store
+inst/doc

DESCRIPTION

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+Package: MIPr
+Title: Collection of Functions for MIPTools Analysis
+Version: 0.0.0.9000
+Authors@R: 
+    person(given = "Aris",
+           family = "Paschalidis",
+           role = c("aut", "cre"),
+           email = "aris.paschalidis@gmail.com",
+           comment = c(ORCID = "0000-0003-2247-1885"))
+Description: What the package does (one paragraph).
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.1.1
+Suggests: 
+    knitr,
+    rmarkdown,
+    spelling
+Language: en-US
+Imports: 
+    dplyr,
+    janitor,
+    magrittr,
+    readr,
+    rlang,
+    tibble,
+    tidyr
+VignetteBuilder: knitr
+Depends: 
+    R (>= 2.10)

LICENSE

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+YEAR: 2021
+COPYRIGHT HOLDER: Aris Paschalidis

LICENSE.md

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+# MIT License
+
+Copyright (c) 2021 Aris Paschalidis
+
+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.

MIPr.Rproj

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+Version: 1.0
+
+RestoreWorkspace: No
+SaveWorkspace: No
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export("%>%")
+export(read)
+importFrom(magrittr,"%>%")
+importFrom(rlang,.data)

R/MIPr.R

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+#' \pkg{MIPr} Collection of Functions for MIPTools Analysis
+#'
+#' @docType package
+#' @name MIPr
+#'
+#' @importFrom rlang .data
+#'
+"_PACKAGE"

R/read.R

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+#------------------------------------------------
+#' Read data
+#'
+#' Read paired data files and combine the files.
+#'
+#' @param alternate_table Alternate table.
+#' @param coverage_table Coverage table.
+#'
+#' @return A tibble containing the parsed data.
+#' @export
+read <- function(alternate_table, coverage_table) {
+  alternate_table <- read_file(alternate_table, "alternate")
+  coverage_table  <- read_file(coverage_table, "coverage")
+
+  bind_table <- dplyr::full_join(alternate_table, coverage_table,
+                                    by = c("sample", "gene_id", "gene",
+                                           "mutation_name", "exonic_func",
+                                           "aa_change", "targeted")) %>%
+    dplyr::mutate(dplyr::across(.data$umi_count:.data$coverage, as.numeric))
+}
+
+#------------------------------------------------
+#' Read file
+#'
+#' Read data files.
+#'
+#' @param file Alternate table.
+#'
+#' @return Parsed file.
+#'
+#' @keywords internal
+read_file <- function(file, type = c("alternate", "coverage")) {
+  data <- readr::read_csv(file, col_names = FALSE) %>%
+    # Take the tranpose of our matrix, making rows columns and columns rows. This
+    # will allows us to keep all the data in our .csv file.
+    tibble::rownames_to_column() %>%
+    tidyr::pivot_longer(-.data$rowname) %>%
+    tidyr::pivot_wider(names_from = .data$rowname,
+                       values_from = .data$value) %>%
+    # Assign the column names of our tibble and clean them up
+    dplyr::select(-.data$name) %>%
+    janitor::row_to_names(1)
+  if (type == "alternate") {
+    data <- data %>%
+      # Convert out data to a long format, where now we have a column with the
+      # umi_count
+      tidyr::pivot_longer(cols = -c(.data$`Gene ID`:.data$Targeted),
+                          names_to = "sample" ,
+                          values_to = "umi_count")
+  } else if (type == "coverage") {
+    data <- data %>%
+      # Convert out data to a long format, where now we have a column with the
+      # coverage
+      tidyr::pivot_longer(cols = -c(.data$`Gene ID`:.data$Targeted),
+                          names_to = "sample" ,
+                          values_to = "coverage")
+  } else {
+    stop("Inocrrect type specified")
+  }
+  data <- data %>%
+    dplyr::relocate(sample) %>%
+    janitor::clean_names()
+}

R/utils-pipe.R

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+#' Pipe operator
+#'
+#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
+#'
+#' @name %>%
+#' @rdname pipe
+#' @keywords internal
+#' @export
+#' @importFrom magrittr %>%
+#' @usage lhs \%>\% rhs
+#' @param lhs A value or the magrittr placeholder.
+#' @param rhs A function call using the magrittr semantics.
+#' @return The result of calling `rhs(lhs)`.
+NULL

README.Rmd

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+---
+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%"
+)
+```
+
+# MIPr
+
+<!-- badges: start -->
+[![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+<!-- badges: end -->
+
+## Installation
+To install the package, please follow the code below. In order to install,
+`devtools` must be installed.
+```{r, eval = FALSE}
+# install.packages("devtools")
+devtools::install_github("https://github.com/arisp099/MIPr")
+```

README.md

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+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# MIPr
+
+<!-- badges: start -->
+
+[![Lifecycle:
+experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![License:
+MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+<!-- badges: end -->
+
+## Installation
+
+To install the package, please follow the code below. In order to
+install, `devtools` must be installed.
+
+``` r
+# install.packages("devtools")
+devtools::install_github("https://github.com/arisp099/MIPr")
+```

inst/WORDLIST

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+MIPTools
+github
+https