revised tests

moved GenomicRanges and IRanges from Suggested packages to imported packages in DESCRIPTION

DESCRIPTION

@@ -12,8 +12,8 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: false
 Depends: R (>= 3.6), data.table (>= 1.12.4), SummarizedExperiment
-Imports: DelayedArray, HDF5Array, BSgenome, rjson, DelayedMatrixStats, parallel, methods, ggplot2, matrixStats, graphics, stats, utils
-RoxygenNote: 7.1.0
+Imports: DelayedArray, HDF5Array, BSgenome, rjson, DelayedMatrixStats, parallel, methods, ggplot2, matrixStats, graphics, stats, utils, GenomicRanges, IRanges
+RoxygenNote: 7.1.1
 Suggests: 
     knitr,
     rmarkdown,
@@ -26,9 +26,7 @@ Suggests:
     GenomicScores,
     Biostrings,
     RColorBrewer,
-    GenomicRanges,
     GenomeInfoDb,
-    IRanges,
     testthat (>= 2.1.0)
 VignetteBuilder: knitr
 biocViews: DNAMethylation, Sequencing, Coverage

R/methrix_operations.R

@@ -31,6 +31,9 @@ get_region_summary = function(m, regions = NULL, type = "M", how = "mean",    ov
 
     start_proc_time = proc.time()
 
+
+    if("data.table" %in% class(regions)) regions<-makeGRangesFromDataFrame(df = regions)
+
     target_regions = (regions)
     #Add a unique id for every target range (i.e, rows)
     target_regions@elementMetadata$rid <- paste0("rid_", 1:length(target_regions))
@@ -39,7 +42,7 @@ get_region_summary = function(m, regions = NULL, type = "M", how = "mean",    ov
     r_dat$seqnames<-as.character(r_dat$chr)
     r_dat$chr<-NULL
     if(is.null(r_dat$end)) r_dat$end<-r_dat$start+1
-    r_dat<-  GenomicRanges::makeGRangesFromDataFrame(r_dat, keep.extra.columns = F)
+    r_dat<-  makeGRangesFromDataFrame(r_dat, keep.extra.columns = F)
 
 
     if(!all(elementMetadata.col %in% colnames(m@elementMetadata))) stop("variables provided to elementMetadata.col not correct")
@@ -121,7 +124,7 @@ get_region_summary = function(m, regions = NULL, type = "M", how = "mean",    ov
 
     output<-output[order(output$rid),]
     setnames(output, "seqnames", "chr")
-    keep=c("chr","start","end","n_overlap_CpGs","rid",elementMetadata.col,colnames(m))
+    keep<-c("chr","start","end","n_overlap_CpGs","rid",elementMetadata.col,colnames(m))
     output<-output[, ..keep]
 
 
@@ -227,8 +230,8 @@ subset_methrix <- function(m, regions = NULL, contigs = NULL, samples = NULL, ov
 #' @details Takes \code{\link{methrix}} object and filters CpGs based on coverage statistics
 #' @param m \code{\link{methrix}} object
 #' @param cov_thr minimum coverage required to call a loci covered
-#' @param min_samples At least these many samples should have a loci with coverage >= \code{cov_thr}. If \code{group} is given, then this applies per group.Only need one of \code{prop_samples} or \code{min_samples}.
-#' @param prop_samples At least this % of samples should have a loci with coverage >= \code{cov_thr}. If \code{group} is given, then this applies per group. Only need one of \code{prop_samples} or \code{min_samples}.
+#' @param min_samples Minimum number of samples that should have a loci with coverage >= \code{cov_thr}. If \code{group} is given, then this applies per group. Only need one of \code{prop_samples} or \code{min_samples}.
+#' @param prop_samples Minimum proportion of samples that should have a loci with coverage >= \code{cov_thr}. If \code{group} is given, then this applies per group. Only need one of \code{prop_samples} or \code{min_samples}.
 #' @param group a column name from sample annotation that defines groups. In this case, the number of min_samples will be
 #' tested group-wise.
 #' @param n_chunks Number of chunks to split the \code{\link{methrix}} object in case it is very large. Default = 1.

R/snp_removal.R

@@ -70,7 +70,7 @@ remove_snps <- function(m, populations = NULL, maf_threshold = 0.01, reduce_filt
     }
 
 
-    regions <- gUtils::gr.nochr(GenomicRanges::makeGRangesFromDataFrame(elementMetadata(m), start.field = "start", end.field = "start"))
+    regions <- gr.nochr(GenomicRanges::makeGRangesFromDataFrame(elementMetadata(m), start.field = "start", end.field = "start"))
 
 
     if(n_cores==1) {

methrix_super_big.Rproj

@@ -0,0 +1,20 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

tests/testthat/test-coverage_filter.R

@@ -28,8 +28,8 @@ test_that("Expected filtering", {
 
 test_that("Expected errors", {
   expect_error(coverage_filter("not methrix", cov_thr = 10, min_samples = 5), "A valid methrix object needs to be supplied.")
-  expect_error(coverage_filter(m1, cov_thr = "not_number", min_samples = 5), "cov_thr and min_samples variables are not numeric.")
-  expect_error(coverage_filter(m1, cov_thr = 10, min_samples = "nn"), "cov_thr and min_samples variables are not numeric.")
+  expect_error(coverage_filter(m1, cov_thr = "not_number", min_samples = 5), "cov_thr is not numeric.")
+  expect_error(coverage_filter(m1, cov_thr = 10, min_samples = "nn"), "min_samples and prop_samples variables are not numeric.")
 
 })
 

tests/testthat/test-get_region_summary.R

@@ -19,19 +19,19 @@ C_max <- apply(get_matrix(methrix_data[1:3,], type = "C", add_loci = FALSE), 2,
 
 test_that("selected regions", {
   expect_equal(as.numeric(get_region_summary(methrix_data,
-                                                regions=gr, type = "M", how = "mean", overlap_type = "any")[1,-(1:4)]), as.numeric(M_mean))
+                                                regions=gr, type = "M", how = "mean", overlap_type = "any")[1,-(1:5)]), as.numeric(M_mean))
   expect_equal(as.numeric(get_region_summary(methrix_data,
-                                                regions=gr, type = "C", how = "mean", overlap_type = "any")[1,-(1:4)]), as.numeric(C_mean))
+                                                regions=gr, type = "C", how = "mean", overlap_type = "any")[1,-(1:5)]), as.numeric(C_mean))
 
   expect_equal(as.numeric(get_region_summary(methrix_data,
-                                                regions=gr, type = "M", how = "min", overlap_type = "any")[1,-(1:4)]), as.numeric(M_min))
+                                                regions=gr, type = "M", how = "min", overlap_type = "any")[1,-(1:5)]), as.numeric(M_min))
   expect_equal(as.numeric(get_region_summary(methrix_data,
-                                                regions=gr, type = "C", how = "min", overlap_type = "any")[1,-(1:4)]), as.numeric(C_min))
+                                                regions=gr, type = "C", how = "min", overlap_type = "any")[1,-(1:5)]), as.numeric(C_min))
 
   expect_equal(as.numeric(get_region_summary(methrix_data,
-                                                regions=gr, type = "M", how = "max", overlap_type = "any")[1,-(1:4)]), as.numeric(M_max))
+                                                regions=gr, type = "M", how = "max", overlap_type = "any")[1,-(1:5)]), as.numeric(M_max))
   expect_equal(as.numeric(get_region_summary(methrix_data,
-                                                regions=gr, type = "C", how = "max", overlap_type = "any")[1,-(1:4)]), as.numeric(C_max))
+                                                regions=gr, type = "C", how = "max", overlap_type = "any")[1,-(1:5)]), as.numeric(C_max))
 })