begin adding main functionality

.Rbuildignore

@@ -11,3 +11,6 @@
 ^appveyor\.yml$
 ^codecov\.yml$
 ^LICENSE\.md$
+^data-raw$
+^inst/extdata/output_simple$
+^inst/extdata/output_consensus$

DESCRIPTION

@@ -19,7 +19,14 @@ Suggests:
  knitr,
  rmarkdown,
  covr,
- spelling
+ spelling,
+ testthat (>= 2.1.0)
 VignetteBuilder: knitr
 RoxygenNote: 6.1.1
 Language: en-US
+Imports: 
+ glue,
+ readr,
+ tibble,
+ dplyr,
+ rlang

NAMESPACE

@@ -1,2 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(conforms_to_delta_fileorg)
+export(get_hn2_subnetworks)
+importFrom(dplyr,"%>%")
+importFrom(rlang,"!!")

R/conforms_to_delta_fileorg.R

@@ -0,0 +1,32 @@
+#' Checks if a directory for a delta value conforms to the expected output
+#'
+#' Returns \code{TRUE} or \{FALSE} for whether a directory conforms to the
+#' expected organization of the delta directory output by HotNet2.
+#'
+#' @param delta_dir The delta directory.
+#'
+#' @return A boolean value for wether the directory conforms to the expected file organization.
+#'
+#' @export conforms_to_delta_fileorg
+conforms_to_delta_fileorg <- function(delta_dir) {
+
+ components_txt <- file.path(delta_dir, "components.txt")
+ if (!check_for_file(components_txt)) return(FALSE)
+
+ results_json <- file.path(delta_dir, "results.json")
+ if (!check_for_file(results_json)) return(FALSE)
+
+ significance_txt <- file.path(delta_dir, "significance.txt")
+ if (!check_for_file(significance_txt)) return(FALSE)
+
+ return(TRUE)
+}
+
+
+check_for_file <- function(fname) {
+ if (!file.exists(fname)) {
+ message(glue::glue("Expected file at {fname} is not available."))
+ return(FALSE)
+ }
+ return(TRUE)
+}

R/get_best_delta.R

@@ -0,0 +1,33 @@
+#' Finds the best delta for a the HotNet2 results
+#'
+#' Briefly, ... (explain how the best delta is chosen). More is explained in the
+#' vignette "...".
+#'
+#' @param delta_tib A data frame (or tibble) with the columns ... for all of the delta values.
+#' @param pval_cutoff The maximum p-value to use for statistical significance.
+#'
+#' @return The best delta value to use or \code{NA} if none can be used.
+#'
+#' @importFrom dplyr %>%
+#' @importFrom rlang !!
+get_best_delta <- function(delta_df, pval_cutoff = 0.05) {
+ delta_best <- delta_df %>%
+ dplyr::group_by(delta) %>%
+ dplyr::summarise(sig_ks = sum(pval < !!pval_cutoff)) %>%
+ dplyr::ungroup() %>%
+ dplyr::filter(sig_ks > 0) %>%
+ dplyr::arrange(dplyr::desc(sig_ks), delta) %>%
+ dplyr::slice(1) %>%
+ dplyr::pull(delta)
+ if (length(delta_best) > 0) {
+ return(delta_best)
+ } else {
+ # if no significant deltas
+ return(NA)
+ }
+}
+
+utils::globalVariables(
+ c("delta", "sig_ks", "pval"),
+ add = TRUE
+)

R/get_hn2_subnetworks.R

@@ -0,0 +1,24 @@
+#' Read in HotNet2 results
+#'
+#' Point this function at the output directory from HotNet2 and it will retrieve
+#' the results from that analysis.
+#'
+#' @param output_dir The output directory from HotNet2.
+#'
+#' @return An S3 object with the parsed results from HotNet2.
+#'
+#' @export get_hn2_subnetworks
+get_hn2_subnetworks <- function(output_dir) {
+
+ # check if the output directory exists
+ if (!dir.exists(output_dir)) {
+ stop(glue::glue("The directory {output_dir} is not accessible or does not exist."))
+ }
+
+
+
+
+
+
+
+}

R/get_k_for_delta.R

@@ -0,0 +1,12 @@
+#' Read in the "k" values for a delta directory
+#'
+#' @param delta_dir The direcotry for a delta value.
+#'
+#' @return A tibble with columns "size", "expected", "actual", and "pval".
+get_k_for_delta <- function(delta_dir) {
+ sig_tib <- readr::read_tsv(
+ paste0(delta_dir, "/significance.txt"),
+ progress = FALSE, col_types = readr::cols())
+ colnames(sig_tib) <- c("size", "expected", "actual", "pval")
+ return(sig_tib)
+}

docs/pkgdown.yml

@@ -1,6 +1,5 @@
 pandoc: 2.7.3
 pkgdown: 1.4.0
 pkgdown_sha: ~
-articles:
- HotNet2-setup-and-example: HotNet2-setup-and-example.html
+articles: []