Merge branch 'devel'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tRavis
 Title: tRavis: an R package by Travis Blimkie
-Version: 1.4.0
+Version: 1.5.12
 Authors@R: person("Travis", "Blimkie", email = "travis.m.blimkie@gmail.com", role = c("aut", "cre"))
 Description: tRavis is a small R package meant to hold functions and data that 
   are used regularly in my day-to-day workflows. Its also provides an 
@@ -22,7 +22,7 @@ Imports:
     stringr,
     tibble,
     tidyr
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests: 
     DESeq2,
     here,

NAMESPACE

@@ -29,3 +29,4 @@ importFrom(stringr,str_wrap)
 importFrom(tibble,as_tibble)
 importFrom(tibble,rownames_to_column)
 importFrom(tidyr,pivot_longer)
+importFrom(utils,read.delim)

R/get_rounded_max.R

@@ -14,20 +14,20 @@
 #'   containing read or count numbers derived from MultiQC, and finds the
 #'   largest read or count value, then round it up to the nearest ten million.
 #'
-#' @details Input data frame must contain the columns "sample" and "n_reads".
+#' @details Input data frame must contain the columns "Samples" and "n_reads".
 #'
 #' @references None.
 #' @seealso <https://www.github.com/travis-m-blimkie/tRavis>
 #'
 get_rounded_max <- function(x, buffer = 1.1, nearest = 10e6) {
   stopifnot(is.data.frame(x))
   stopifnot(
-    "'x' must contain columns 'sample' and 'n_reads'." =
-      c("sample", "n_reads") %in% colnames(x)
+    "'x' must contain columns 'Samples' and 'n_reads'." =
+      c("Samples", "n_reads") %in% colnames(x)
   )
 
   max_value <- x %>%
-    group_by(sample) %>%
+    group_by(Samples) %>%
     summarise(sum_n_reads = sum(n_reads)) %>%
     pull(sum_n_reads) %>%
     max()

R/globals.R

@@ -4,11 +4,14 @@ utils::globalVariables(c(
   "ambiguous",
   "assigned",
   "duplicate",
+  "duplicate_reads",
   "end",
   "gene_name",
   "is",
   "locus_tag",
   "log2FoldChange",
+  "mapped_to_multiple_loci",
+  "mapped_to_too_many_loci",
   "multimapped",
   "multimapped_toomany",
   "n_reads",
@@ -24,7 +27,9 @@ utils::globalVariables(c(
   "qc",
   "read_type",
   "Read type",
+  "sample",
   "Sample",
+  "Samples",
   "start",
   "strand",
   "sum_n_reads",
@@ -33,7 +38,9 @@ utils::globalVariables(c(
   "total_deduplicated_percentage",
   "total_reads",
   "total_sequences",
+  "unique_reads",
   "uniquely_mapped",
   "unmapped_other",
-  "unmapped_tooshort"
+  "unmapped_tooshort",
+  "unmapped_too_short"
 ))

R/tr_compare_lists.R

@@ -3,7 +3,7 @@
 #' @param x First vector to compare.
 #' @param y Second vector to compare.
 #' @param names Optional character vector, containing names of `x` and `y` to
-#'   apply to the output.
+#'   apply to the output. Defaults to NULL for no names.
 #'
 #' @return A named list of the common and unique elements of x and y.
 #' @export

R/tr_get_files.R

@@ -10,7 +10,7 @@
 #'   formatted akin to "YYYYMMDD", i.e. all numeric with no spaces, dashes, etc.
 #'   Defaults to FALSE.
 #' @param remove_string Optional string which can be removed from file names
-#'   when creating names for the output list
+#'   when creating names for the output list. Defaults to NULL for no changes.
 #'
 #' @return Named list of files
 #' @export