bump version to v1.2.5

ShixiangWang · Feb 19, 2021 · 70108c6 · 70108c6
1 parent d3ae8d4
commit 70108c6
Show file tree

Hide file tree

Showing 121 changed files with 342 additions and 157 deletions.
diff --git a/CRAN-RELEASE b/CRAN-RELEASE
@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2021-01-30.
-Once it is accepted, delete this file and tag the release (commit d8de0ae).
+This package was submitted to CRAN on 2021-02-19.
+Once it is accepted, delete this file and tag the release (commit d3ae8d4).
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: sigminer
 Title: Extract, Analyze and Visualize Mutational Signatures for
     Genomic Variations
-Version: 1.2.4.999
+Version: 1.2.5
 Authors@R: 
     c(person(given = "Shixiang",
              family = "Wang",

diff --git a/NAMESPACE b/NAMESPACE
@@ -55,7 +55,7 @@ export(output_tally)
 export(read_copynumber)
 export(read_copynumber_seqz)
 export(read_maf)
-export(read_rs)
+export(read_sv_as_rs)
 export(read_vcf)
 export(read_xena_variants)
 export(report_bootstrap_p_value)

diff --git a/NEWS.md b/NEWS.md
@@ -2,14 +2,15 @@
 
 ## BUG REPORTS
 
-
 ## ENHANCEMENTS
 
 - Modified the default visualization of `bp_show_survey()`.
 - Enhanced `torch` check.
 
 ## NEW FUNCTIONS
 
+- `read_sv_as_rs()` and `sig_tally.RS()` for simplified genome rearrangement classification matrix generation (experimental).
+
 ## DEPRECATED
 
 # sigminer 1.2.4

diff --git a/R/get_sv.R b/R/get_sv.R
@@ -9,14 +9,14 @@
 #'
 #' @examples
 #' sv <- readRDS(system.file("extdata", "toy_sv.rds", package = "sigminer", mustWork = TRUE))
-#' rs <- read_rs(sv)
+#' rs <- read_sv_as_rs(sv)
 #' \donttest{
 #' tally_rs <- sig_tally(rs)
 #' }
 #' @testexamples
 #' expect_is(rs, "RS")
 #' expect_is(tally_rs, "list")
-read_rs <- function(input) {
+read_sv_as_rs <- function(input) {
   if (is.data.frame(x = input)) {
     input <- data.table::as.data.table(input)
   } else {
@@ -65,19 +65,15 @@ read_rs <- function(input) {
 }
 
 # split by sample and collect in a list : svlist --------------------------
-# imitate : sigminer::get_cnlist()
 get_svlist <- function(data) {
   index <- seq(1, nrow(data))
   data$Index <- index
   res <- split(data, by = "sample")
 }
 
-
 # get size
 getRearrSize_v1 <- function(sv_profiles) {
-  # sv_profiles <- svlist
   rearrsize <- purrr::map_df(sv_profiles, function(x) {
-    # x <- sv_profiles$PD26851a[1]
     if (x$svclass == "translocation") x$rearrsize <- NA
     length <- x$end2 - x$start1
     if (length < 1000) x$rearrsize <- "<1Kb"
@@ -95,9 +91,6 @@ getRearrSize_v1 <- function(sv_profiles) {
   rearrsize[order(rearrsize$Index)]
 }
 
-
-
-
 # copy from UCL-Research-Department-of-Pathology/RESIN --------------------
 getDists <- function(chrom1, pos1, chrom2, pos2, doPCF = FALSE) {
   pos1 <- as.numeric(pos1)
@@ -129,13 +122,8 @@ getDists <- function(chrom1, pos1, chrom2, pos2, doPCF = FALSE) {
   return(dists)
 }
 
-
-
 # get clustered -----------------------------------------------------------
 getClustered_v1 <- function(sv_profiles, threshold = NULL) {
-  # sv_profiles <- svlist
-  # x <- sv_profiles$PD26879a
-  # x <- sv_profiles$PD26851a
   # threshold = NULL
   # each list each row apply function
   clustered <- purrr::map(sv_profiles, function(x) {
@@ -193,10 +181,7 @@ getType_v1 <- function(sv_profiles) {
 }
 
 
-
-
 # get features list -------------------------------------------------------
-# imitate : get_features_wang
 get_features_sv <- function(sv_data) {
   field <- c(
     "clustered",
@@ -255,8 +240,6 @@ call_component <- function(f_dt, f_name) {
 }
 
 
-
-
 # get sv matrix
 get_matrix_sv <- function(CN_components, indices = NULL) {
   merged_dt <- purrr::reduce(CN_components, merge, by = c("sample", "Index"), all = TRUE)
@@ -288,7 +271,7 @@ get_matrix_sv <- function(CN_components, indices = NULL) {
   sv_mat_32 <- sv_mat[, !(grepl("<1Kb", colnames(sv_mat)))]
 
   return(list(
-    SV_32 = sv_mat_32,
-    SV_38 = sv_mat
+    RS_32 = sv_mat_32,
+    RS_38 = sv_mat
   ))
 }
diff --git a/R/sig_tally.R b/R/sig_tally.R
@@ -27,7 +27,7 @@
 #' set `sigminer.copynumber.max` to a proper value (the best is consistent
 #' with [read_copynumber]).
 #'
-#' @param object a [CopyNumber] object or [MAF] object or SV object (from [read_sv]).
+#' @param object a [CopyNumber] object or [MAF] object or SV object (from [read_sv_as_rs]).
 #' @param ... custom setting for operating object. Detail see S3 method for
 #' corresponding class (e.g. `CopyNumber`).
 #' @return a `list` contains a `matrix` used for NMF de-composition.
@@ -395,25 +395,25 @@ sig_tally.CopyNumber <- function(object,
   }
 }
 
-#' @describeIn sig_tally Returns rearrangement sample-by-component matrix
+#' @describeIn sig_tally Returns genome rearrangement sample-by-component matrix
 #' @export
 sig_tally.RS <- function(object, keep_only_matrix = FALSE, ...) {
   svlist <- get_svlist(object)
-  message("Successfully get RS list!")
+  send_success("Successfully get RS list!")
 
   sv_features <- get_features_sv(svlist)
-  message("Successfully get RS features!")
+  send_success("Successfully get RS features!")
 
   sv_component <- get_components_sv(sv_features)
-  message("Successfully get RS component!")
+  send_success("Successfully get RS component!")
 
   sv_matrix_list <- get_matrix_sv(CN_components = sv_component)
-  message("Successfully get RS matrix!")
+  send_success("Successfully get RS matrix!")
 
   res_list <- list(
     features = sv_features,
     components = sv_component,
-    nmf_matrix = sv_matrix_list$SV_32,
+    nmf_matrix = sv_matrix_list$RS_32,
     all_matrices = sv_matrix_list
   )
 

diff --git a/README.Rmd b/README.Rmd
@@ -84,7 +84,6 @@ p5 <- show_cosmic_sig_profile(sig_index = c("R1", "R2", "R3"), sig_db = "RS_Nik_
 p5
 ```
 
-> `sig_tally()` for RS is not supported.
 
 ### Features
 

diff --git a/README.md b/README.md
@@ -50,8 +50,6 @@ For pipeline tool, please see its co-evolutionary CLI
 
 <img src="man/figures/README-unnamed-chunk-5-1.png" width="100%" />
 
-> `sig_tally()` for RS is not supported.
-
 ### Features
 
 -   supports a standard *de novo* pipeline for identification of **5**

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -15,6 +15,7 @@ reference:
     - read_copynumber
     - read_copynumber_seqz
     - read_maf
+    - read_sv_as_rs
     - read_vcf
     - read_xena_variants
     - CopyNumber-class

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/README_zh.html b/docs/README_zh.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/sigminer.html b/docs/articles/sigminer.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,5 +3,5 @@ pkgdown: 1.6.1
 pkgdown_sha: ~
 articles:
   sigminer: sigminer.html
-last_built: 2021-01-30T07:36Z
+last_built: 2021-02-19T14:40Z
 
diff --git a/docs/reference/CN.features.html b/docs/reference/CN.features.html
diff --git a/docs/reference/CopyNumber-class.html b/docs/reference/CopyNumber-class.html
diff --git a/docs/reference/MAF-class.html b/docs/reference/MAF-class.html
diff --git a/docs/reference/add_h_arrow.html b/docs/reference/add_h_arrow.html
diff --git a/docs/reference/add_labels.html b/docs/reference/add_labels.html
diff --git a/docs/reference/bp.html b/docs/reference/bp.html
diff --git a/docs/reference/centromeres.hg19.html b/docs/reference/centromeres.hg19.html