Merge pull request #11 from stemangiola/fix-zero-sigma

Fix zero sigma

Author: stemangiola

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ppcseq
 Title: Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models
-Version: 0.99.7
+Version: 0.99.16
 Authors@R: 
     person(given = "Stefano",
            family = "Mangiola",
@@ -28,7 +28,7 @@ Encoding: UTF-8
 LazyData: true
 Biarch: true
 Depends: 
-    R (>= 4.0.0)
+    R (>= 4.1.0)
 Imports: 
     methods,
     Rcpp (>= 0.12.0),
@@ -49,7 +49,9 @@ Imports:
     benchmarkme,
     parallel,
     rlang,
-    stats 
+    stats,
+    utils,
+    graphics
 LinkingTo: 
     BH (>= 1.66.0),
     Rcpp (>= 0.12.0),
@@ -59,7 +61,8 @@ LinkingTo:
 Suggests: 
     knitr,
     testthat,
-    BiocStyle
+    BiocStyle,
+    rmarkdown
 VignetteBuilder: 
     knitr
 RdMacros:

R/ppcseq-package.R

@@ -15,7 +15,7 @@
 #'
 #' @usage data(counts)
 #'
-#'
+#' @return See documentation
 #'
 #' @references
 #' Stan Development Team (2019). RStan: the R interface to Stan. R package version 2.19.2. https://mc-stan.org

R/ppcseq.R

@@ -52,6 +52,7 @@
 #'
 #' data("counts")
 #'
+#' if(Sys.info()[['sysname']] != "Windows")
 #' result =
 #'   counts %>%
 #'   dplyr::mutate(  is_significant = ifelse(symbol %in% c("SLC16A12", "CYP1A1", "ART3"), TRUE, FALSE) ) %>%
@@ -140,7 +141,7 @@ identify_outliers = function(.data,
 		stop("There are NAs in the .transcript. Please filter those records")
 
 	# Check if the counts column is an integer
-	if (.data %>% select(!!.abundance) %>% map_chr(~ class(.x)) != "integer")
+	if (.data %>% pull(!!.abundance) %>% is("integer") %>% not())
 		stop(
 			sprintf(
 				"The column %s must be of class integer. You can do as mutate(`%s` = `%s` %%>%% as.integer)",
@@ -375,6 +376,7 @@ identify_outliers = function(.data,
 #'
 #' data("counts")
 #'
+#' if(Sys.info()[['sysname']] != "Windows"){
 #' result =
 #'   counts %>%
 #'   dplyr::mutate(  is_significant = ifelse(symbol %in% c("SLC16A12", "CYP1A1", "ART3"), TRUE, FALSE) ) %>%
@@ -392,6 +394,7 @@ identify_outliers = function(.data,
 #'	)
 #'
 #' result_plot = result %>% plot_credible_intervals()
+#' }
 #'
 #' @export
 #'

R/utilities.R

@@ -1184,7 +1184,7 @@ identify_outliers_1_step = function(.data,
 		stop("There are NAs in the .transcript. Please filter those records")
 
 	# Check if the counts column is an integer
-	if (.data %>% select(!!.abundance) %>% map_chr(~ class(.x)) != "integer")
+	if (.data %>% pull(!!.abundance) %>% is("integer") %>% not())
 		stop(
 			sprintf(
 				"The column %s must be of class integer. You can do as mutate(`%s` = `%s` %%>%% as.integer)",

inst/stan/negBinomial_MPI.stan

@@ -80,6 +80,14 @@ functions{
 		// Vectorise lpmf
 		//vector[symbol_end[G_per_shard+1]] lambda_MPI_c;
 		vector[symbol_end[G_per_shard+1]] sigma_MPI_c;
+
+		// print(rows(local_parameters));
+		// print(local_parameters);
+		// print("----");
+		// print(lambda_MPI);
+		// print(sigma_MPI);
+		// print(exposure_rate);
+
 		for(g in 1:G_per_shard){
 			int how_many = symbol_end[g+1] - (symbol_end[g]);
 			//lambda_MPI_c[(symbol_end[g]+1):symbol_end[g+1]] = rep_vector(lambda_MPI[g], how_many);

man/identify_outliers.Rd

@@ -2,6 +2,8 @@ context('ppcseq')
 
 data("counts")
 
+if(Sys.info()[['sysname']] != "Windows"){
+
 test_that("VB post approx no correction",{
 
   res =
@@ -28,31 +30,6 @@ test_that("VB post approx no correction",{
 
 })
 
-test_that("VB post approx yes correction",{
-
-  res =
-    ppcseq::identify_outliers(
-      dplyr::mutate(counts,  is_significant = ifelse(symbol %in% c("SLC16A12", "CYP1A1", "ART3"), TRUE, FALSE) ),
-      formula = ~ Label,
-      sample, symbol, value,
-      .significance = PValue,
-      .do_check  = is_significant,
-      percent_false_positive_genes = 1,
-      tol_rel_obj = 0.01,
-      approximate_posterior_inference =TRUE,
-      approximate_posterior_analysis =TRUE,
-      how_many_negative_controls = 50,
-      cores=1,pass_fit = TRUE
-    )
-
-  expect_equal(
-
-    as.integer(unlist(res[,4])),
-    c(0,1,0)
-  )
-
-})
-
 test_that("VB post full",{
 
   res =
@@ -78,3 +55,6 @@ test_that("VB post full",{
 
 })
 
+} else{
+  print("tests for windows are temporarily disabled")
+}