test data updates

R/VLPFractionSamplePileup.R

@@ -26,16 +26,21 @@
 #' pileup file with 100 bp windows. A subset of 10 contigs from the pileup file
 #' were selected for this sample dataset. The contigs were chosen because their
 #' associated read coverage patterns in the VLP-fraction exemplify TrIdent's
-#' pattern-matching functionality across classifications: NODE_617:
-#' Prophage-like, active/abundant, with spec transduction NODE_125:
-#' Prophage-like, off one side of contig, no spec transduction NODE_352:
-#' Sloping, left to right slope NODE_251: Sloping, right to left slope
-#' NODE_2060: Sloping, right to left slope with start NODE_1401: None, no
-#' pattern match NODE_62: Prophage-like, with spec transduction NODE_368:
-#' Prophage-like, not homogeneously integrated/present, no spec transduction
-#' NODE_560: HighCovNoPattern NODE_1165: None, filtered out To access the
-#' sequencing data used to generate this pileup file and for additional details
-#' on the assembly and mapping parameters, refer to the reference below:
+#' pattern-matching functionality across classifications:
+#' NODE_617:Prophage-like, active/abundant, with spec transduction
+#' NODE_125:Prophage-like, off one side of contig, no spec transduction
+#' NODE_352:Sloping, left to right slope
+#' NODE_251: Sloping, right to left slope
+#' NODE_2060: Sloping, right to left slope with start
+#' NODE_1401: None, no pattern match
+#' NODE_62: Prophage-like, with spec transduction
+#' NODE_368: Prophage-like, not homogeneously integrated/present, no spec
+#' transduction
+#' NODE_560: HighCovNoPattern
+#' NODE_1165: None, filtered out
+#' To access the sequencing data used to generate this pileup file and for
+#' additional details on the assembly and mapping parameters, refer to the
+#' reference below:
 #' Reference: Kleiner, M., Bushnell, B., Sanderson, K.E. et al. Transductomics:
 #' sequencing-based detection and analysis of transduced DNA in pure cultures
 #' and microbial communities. Microbiome 8, 158 (2020).

R/WholeCommunitySamplePileup.R

@@ -27,15 +27,20 @@
 #' selected for this sample dataset. The contigs were chosen because their
 #' associated read coverage patterns in the VLP-fraction exemplify TrIdent's
 #' pattern-matching and characterization functionality across classifications:
-#' NODE_617: Prophage-like, active/abundant, with spec transduction NODE_125:
-#' Prophage-like, off one side of contig, no spec transduction NODE_352:
-#' Sloping, left to right slope NODE_251: Sloping, right to left slope
-#' NODE_2060: Sloping, right to left slope with start NODE_1401: None, no
-#' pattern match NODE_62: Prophage-like, with spec transduction NODE_368:
-#' Prophage-like, not homogeneously integrated/present, no spec transduction
-#' NODE_560: HighCovNoPattern NODE_1165: None, filtered out To access the
-#' sequencing data used to generate this pileup file and for additional details
-#' on the assembly and mapping parameters, refer to the reference below:
+#' NODE_617:Prophage-like, active/abundant, with spec transduction
+#' NODE_125:Prophage-like, off one side of contig, no spec transduction
+#' NODE_352:Sloping, left to right slope
+#' NODE_251: Sloping, right to left slope
+#' NODE_2060: Sloping, right to left slope with start
+#' NODE_1401: None, no pattern match
+#' NODE_62: Prophage-like, with spec transduction
+#' NODE_368: Prophage-like, not homogeneously integrated/present, no spec
+#' transduction
+#' NODE_560: HighCovNoPattern
+#' NODE_1165: None, filtered out
+#' To access the sequencing data used to generate this pileup file and for
+#' additional details on the assembly and mapping parameters, refer to the
+#' reference below:
 #' Reference: Kleiner, M., Bushnell, B., Sanderson, K.E. et al. Transductomics:
 #' sequencing-based detection and analysis of transduced DNA in pure cultures
 #' and microbial communities. Microbiome 8, 158 (2020).

R/prophageLikeBorders.R

@@ -9,7 +9,7 @@
 #' @param classificationPatterns The pattern match information associated with
 #'   each contig classified as Prophage-like, Sloping, or HighCovNoPattern
 #' @param i The index for the contig currently being assessed
-#' @param windowsize The window size used to re-average read coverage pileups
+#' @param windowSize The window size used to re-average read coverage pileups
 #' @return List
 #' @importFrom roll roll_sd
 #' @keywords internal

tests/testthat/test-specializedTransductionID.R

@@ -1,5 +1,5 @@
 test_that("specializedTransductionID", {
-    data("VLPFractionSamplePileup")
+  data("VLPFractionSamplePileup")
     data("WholeCommunitySamplePileup")
     TrIdent_results <- TrIdentClassifier(
         VLPpileup = VLPFractionSamplePileup,
@@ -29,10 +29,3 @@ test_that("specializedTransductionID", {
         copied_Specialized_transduction_NODE62$Plots$plot
     )
 })
-
-# test_that("SpecializedTransduction_ID_Node_44", {
-#  TrIdent_results <- TrIdentClassifier(VLP_pileup=VLPFractionSampleData, WC_pileup=WholeCommunitySamplePileup, windowsize=1000, minblocksize=10000, maxblocksize=Inf, cleanup=TRUE)
-#  temp_Specialized_transduction_n44 <- SpecializedTransduction_ID(VLP_pileup=VLPFractionSampleData, transductionclassifications=TrIdent_results, specificcontig="NODE_44", noreadcov=500, spectranslength=2000, cleanup=TRUE)
-#  copied_Specialized_transduction_NODE44 <- Specialized_transduction_NODE44
-#  expect_equal(temp_Specialized_transduction_n44$Plots$plot, copied_Specialized_transduction_NODE44$Plots$plot)
-# })