Test data updates

jlmaier12 · Dec 18, 2024 · 3944e80 · 3944e80
1 parent 7ab4fa9
commit 3944e80
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Showing 8 changed files with 6 additions and 5 deletions.
diff --git a/R/VLPFractionSamplePileup.R b/R/VLPFractionSamplePileup.R
@@ -28,7 +28,7 @@
 #' 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_135: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

diff --git a/R/WholeCommunitySamplePileup.R b/R/WholeCommunitySamplePileup.R
@@ -28,7 +28,7 @@
 #' 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_135: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

diff --git a/R/noPattern.R b/R/noPattern.R
@@ -14,7 +14,8 @@ noPattern <- function(viralSubset) {
     diff1 <- mean(abs(viralSubset[, 2] - pattern1))
     diff2 <- mean(abs(viralSubset[, 2] - pattern2))
     diff <- ifelse(diff1 < diff2, diff1, diff2)
-    value <- ifelse(diff1 < diff2, median(viralSubset[, 2]), mean(viralSubset[, 2]))
+    value <- ifelse(diff1 < diff2, median(viralSubset[, 2]),
+                    mean(viralSubset[, 2]))
     bestMatchInfo <-
         list(
             diff,

diff --git a/data/TrIdentSampleOutput.rda b/data/TrIdentSampleOutput.rda
diff --git a/data/VLPFractionSamplePileup.rda b/data/VLPFractionSamplePileup.rda
diff --git a/data/WholeCommunitySamplePileup.rda b/data/WholeCommunitySamplePileup.rda
diff --git a/man/VLPFractionSamplePileup.Rd b/man/VLPFractionSamplePileup.Rd
diff --git a/man/WholeCommunitySamplePileup.Rd b/man/WholeCommunitySamplePileup.Rd