Purge subsampling test code.

DESCRIPTION

@@ -9,6 +9,7 @@ Description: Provides functions for hit gene identification and  quantification
   Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>. 
 Depends: R (>= 3.5.0)
 License: MIT + file LICENSE
+LazyData: true
 Imports:
   Rcpp (>= 0.12.16), 
     metap,

NAMESPACE

@@ -1,5 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
+export(calc_mappability)
+export(fit_ab)
+export(get_CPM)
+export(measure_gene_stats)
+export(measure_sgrna_stats)
+export(plot_PCA)
+export(plot_corr_heatmap)
+export(plot_count_distribution)
+export(plot_dotplot)
+export(quant)
+export(run_estimation)
+export(run_sgrna_quant)
 importFrom(Rcpp,evalCpp)
 importFrom(dplyr,arrange_)
 importFrom(dplyr,group_by)

R/data.R

@@ -10,6 +10,11 @@
 #'   \item{sg_stat}{The data.frame contains the sgRNA-level statistics.}
 #'   \item{gene_stat}{The data.frame contains the gene-level statistics.}
 #' }
+#' 
+#' @docType data
+#'
+#' @usage data(Evers_CRISPRn_RT112)
+#'
 #' @source \url{https://www.ncbi.nlm.nih.gov/pubmed/27111720}
 "Evers_CRISPRn_RT112"
 
@@ -24,5 +29,10 @@
 #'   \item{ngenes}{The list of 927 non-essential genes used in Sanson et al.'s study.}
 #'   \item{design}{The data.frame contains study design.}
 #' }
+#' 
+#' @docType data
+#'
+#' @usage data(Sanson_CRISPRn_A375)
+#'
 #' @source \url{https://www.ncbi.nlm.nih.gov/pubmed/30575746}
 "Sanson_CRISPRn_A375"

tests/testthat/test.toydata.R

@@ -41,26 +41,6 @@ test_that("A very simple sanity check", {
 })
 
 
-test_that("Testing whether subsamplings with the same seed are identical.", {
-  set.seed(123)
-  cb2_count <- run_sgrna_quant(FASTA, df_design, sampling_ratio = 0.5)
-
-  set.seed(123)
-  cb2_count2 <- run_sgrna_quant(FASTA, df_design, sampling_ratio = 0.5)
-
-  expect_identical(cb2_count, cb2_count2)
-})
-
-test_that("Testing whether the subsampling code works as intended.", {
-  cb2_count_nosubs <- run_sgrna_quant(FASTA, df_design)
-
-  for( i in seq(0.1, 0.9, 0.1)) {
-    set.seed(123)
-    cb2_count <- run_sgrna_quant(FASTA, df_design, sampling_ratio = i)
-    expect_equal(sum(dplyr::between(cb2_count$total / cb2_count_nosubs$total, i-0.1, i+0.1)), length(cb2_count$total))
-  }
-})
-
 # test_that("The result has to be consistent to the publication", {
 #   data("Sanson_CRISPRn_A375")
 #   published <- read.csv("https://raw.githubusercontent.com/hyunhwaj/CB2-Experiments/master/01_gene-level-analysis/results/Sanson/CRISPRn-A375/FDR/CB2.csv")