Support separated index, related to ShixiangWang/sigflow#11

NEWS.md

@@ -1,5 +1,6 @@
 # sigminer 1.0.14
 
+- Supported signature index separated by `,` in `sig_fit()` and `sig_fit_bootstrap*` functions.
 - Added `output_*` functions from [sigflow](https://github.com/ShixiangWang/sigminer.workflow).
 - Enhanced DBS search and error handling in `sig_tally()`.
 - Added option `highlight_genes` in `show_cn_group_profile()` to show gene labels.

R/sig_fit.R

@@ -112,6 +112,7 @@ sig_fit <- function(catalogue_matrix,
   on.exit(send_elapsed_time(timer))
 
   if (is.null(sig_index)) {
+    send_info("Signature index not detected.")
     if (inherits(sig, "Signature")) {
       send_success("Signature object detected.")
       sig_matrix <- sig$Signature
@@ -167,6 +168,13 @@ sig_fit <- function(catalogue_matrix,
       sig_index <- avail_index
     }
 
+    if (length(sig_index) == 1) {
+      if (grepl(",", sig_index)) {
+        send_success("Signature indices separated by comma are detected.")
+        sig_index <- split_seq(sig_index)
+      }
+    }
+
     if (!all(sig_index %in% avail_index)) {
       send_error("Invalid index.")
       send_info(msg)

R/sig_fit_bootstrap_batch.R

@@ -1,5 +1,7 @@
 #' Exposure Instability Analysis of Signature Exposures with Bootstrapping
 #'
+#' Read [sig_fit_bootstrap] for more option setting.
+#'
 #' @inheritParams sig_fit
 #' @inheritParams sig_fit_bootstrap
 #' @param methods a subset of `c("NNLS", "QP", "SA")`.