Fix example references to renamed odds_ratios_filtered files

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: jayhesselberth

R/plot-chord.R

@@ -41,7 +41,7 @@
 #' @examples
 #' \donttest{
 #' path <- clover_example(
-#'   "ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.odds_ratios.tsv.gz"
+#'   "ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.odds_ratios_filtered.tsv.gz"
 #' )
 #' or_data <- read_odds_ratios(path)
 #' or_data <- dplyr::filter(or_data, ref == "host-tRNA-Glu-TTC-1-1")

R/read-charging.R

@@ -27,7 +27,7 @@ read_charging <- function(path) {
 #' Read a per-position-pair odds ratio file produced by the tRNA sequencing
 #' pipeline. These files contain pairwise modification co-occurrence statistics.
 #'
-#' @param path Path to a `{sample}.odds_ratios.tsv.gz` file.
+#' @param path Path to a `{sample}.odds_ratios_filtered.tsv.gz` file.
 #'
 #' @return A tibble with columns including `ref`, `pos1`, `pos2`,
 #'   `odds_ratio`, `log_odds_ratio`, `p_value`, and `total_obs`.
@@ -36,7 +36,7 @@ read_charging <- function(path) {
 #'
 #' @examples
 #' path <- clover_example(
-#'   "ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.odds_ratios.tsv.gz"
+#'   "ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.odds_ratios_filtered.tsv.gz"
 #' )
 #' read_odds_ratios(path)
 read_odds_ratios <- function(path) {
@@ -106,10 +106,10 @@ read_charging_multi <- function(paths) {
 #' @examples
 #' paths <- c(
 #'   "wt-15-ctl-01" = clover_example(
-#'     "ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.odds_ratios.tsv.gz"
+#'     "ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.odds_ratios_filtered.tsv.gz"
 #'   ),
 #'   "wt-15-ctl-02" = clover_example(
-#'     "ecoli/summary/tables/wt-15-ctl-02/wt-15-ctl-02.odds_ratios.tsv.gz"
+#'     "ecoli/summary/tables/wt-15-ctl-02/wt-15-ctl-02.odds_ratios_filtered.tsv.gz"
 #'   )
 #' )
 #' read_odds_ratios_multi(paths)

man/clover-package.Rd

@@ -264,7 +264,7 @@ magnitude.
 ```{r}
 #| label: linkages-setup
 or_path <- clover_example(
-  "ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.odds_ratios.tsv.gz"
+  "ecoli/summary/tables/wt-15-ctl-01/wt-15-ctl-01.odds_ratios_filtered.tsv.gz"
 )
 or_data <- read_odds_ratios(or_path)