update doc

ShixiangWang · Mar 15, 2023 · 41a23cd · 41a23cd
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diff --git a/R/sig_tally.R b/R/sig_tally.R
@@ -122,7 +122,8 @@ sig_tally <- function(object, ...) {
 #' @describeIn sig_tally Returns copy number features, components and component-by-sample matrix
 #' @param indices integer vector indicating segments to keep.
 #' @param method method for feature classification, can be one of
-#' "Wang" ("W"), "S" (for method described in Steele et al. 2019).
+#' "Wang" ("W"), "S" (for method described in Steele et al. 2019),
+#' "X" (for method described in Tao et al. 2023).
 #' @param add_loh flag to add LOH classifications.
 #' @param feature_setting a `data.frame` used for classification.
 #' **Only used when method is "Wang" ("W")**.
@@ -153,7 +154,6 @@ sig_tally.CopyNumber <- function(object,
   method <- match.arg(method, choices = c("Wang", "W", "Tao & Wang", "T", "X", "S"))
 
   if (startsWith(method, "T") | method == "X") {
-    send_warning("Currently, the method 'T' is in experimental stage, please don't use it for now!")
     ## Add segment index for method "T" so the segments can be easily joined or checked
     cn_list <- get_cnlist(object, ignore_chrs = ignore_chrs, add_index = TRUE)
   } else {

diff --git a/man/show_cn_components.Rd b/man/show_cn_components.Rd
diff --git a/man/show_cn_features.Rd b/man/show_cn_features.Rd
diff --git a/man/sig_tally.Rd b/man/sig_tally.Rd
diff --git a/vignettes/cnsignature.Rmd b/vignettes/cnsignature.Rmd
@@ -16,6 +16,8 @@ knitr::opts_chunk$set(
 )
 ```
 
+> Exploring copy number signatures with recently developed approach have been described at [The repertoire of copy number alteration signatures in human cancer](https://xsliulab.github.io/Pan-cancer_CNA_signature/).
+>
 > A more general introduction please read [Extract, Analyze and Visualize Mutational Signatures with Sigminer](https://shixiangwang.github.io/sigminer-book/index.html).
 
 ```{r setup}
-Original file line number
+Diff line change
@@ Expand Up / @@ -16,6 +16,8 @@ knitr::opts_chunk$set( @@
     )
     ```
+    > Exploring copy number signatures with recently developed approach have been described at [The repertoire of copy number alteration signatures in human cancer](https://xsliulab.github.io/Pan-cancer_CNA_signature/).
+    >
     > A more general introduction please read [Extract, Analyze and Visualize Mutational Signatures with Sigminer](https://shixiangwang.github.io/sigminer-book/index.html).
     ```{r setup}
@@ Expand Down @@