release v0.1.5

ShixiangWang · Jan 30, 2019 · 4d6ad0c · 4d6ad0c
1 parent ed6c0a9
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diff --git a/NAMESPACE b/NAMESPACE
@@ -22,6 +22,7 @@ export(get_matrix)
 export(hello)
 export(prepare_copynumber)
 export(read_copynumber)
+export(read_maf)
 export(read_variation)
 export(sig_assign_samples)
 export(sig_estimate)

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,12 @@
 # sigminer v0.1.5
 
-* update intro for package
+* update introduction for package `sigminer`
 * fix text problem provided by CRAN check team
 * add `sig_get_similarity` function
+* add toy datasets & update examples 
+* fix typo in `sig_assign_samples`
+* export `read_maf` 
+* update README
 
 # sigminer v0.1.4
 

diff --git a/R/draw_series.R b/R/draw_series.R
@@ -18,17 +18,13 @@
 #' @import ggplot2
 #' @export
 #' @examples
-#' \donttest{
-#' load(system.file("extdata", "example_cn_list.RData",
-#'      package = "sigminer", mustWork = TRUE))
-#' segTabs = data.table::rbindlist(tcga_segTabs, idcol = "sample")
-#' cn = read_copynumber(segTabs,
-#'                      seg_cols = c("chromosome", "start", "end", "segVal"),
-#'                      genome_build = "hg19")
+#' # Load copy number object
+#' load(system.file("extdata", "toy_copynumber.RData",
+#'              package = "sigminer", mustWork = TRUE))
+#' # Plot distribution
 #' draw_cn_distribution(cn)
 #' draw_cn_distribution(cn, mode = "cd")
 #' draw_cn_distribution(cn, mode = "cd", fill = TRUE)
-#' }
 #' @family copy number plot
 draw_cn_distribution = function(data,
                                 rm_normal = TRUE,
@@ -169,16 +165,10 @@ draw_cn_distribution = function(data,
 #' @import ggplot2
 #' @family copy number plot
 #' @examples
-#' \donttest{
-#' load(system.file("extdata", "example_cn_list.RData",
-#'      package = "sigminer", mustWork = TRUE))
-#' segTabs = data.table::rbindlist(tcga_segTabs, idcol = "sample")
-#' cn = read_copynumber(segTabs,
-#'                      seg_cols = c("chromosome", "start", "end", "segVal"),
-#'                      genome_build = "hg19")
-#' cn_prepare =  sig_prepare(cn)
+#' # Load copy number prepare object
+#' load(system.file("extdata", "toy_copynumber_prepare.RData",
+#'              package = "sigminer", mustWork = TRUE))
 #' draw_cn_features(cn_prepare$features)
-#' }
 #' @export
 #'
 draw_cn_features = function(features, ylab = "", ...) {
@@ -243,16 +233,10 @@ draw_cn_features = function(features, ylab = "", ...) {
 #' @import ggplot2
 #' @export
 #' @examples
-#' \donttest{
-#' load(system.file("extdata", "example_cn_list.RData",
-#'      package = "sigminer", mustWork = TRUE))
-#' segTabs = data.table::rbindlist(tcga_segTabs, idcol = "sample")
-#' cn = read_copynumber(segTabs,
-#'                      seg_cols = c("chromosome", "start", "end", "segVal"),
-#'                      genome_build = "hg19")
-#' cn_prepare =  sig_prepare(cn)
+#' # Load copy number prepare object
+#' load(system.file("extdata", "toy_copynumber_prepare.RData",
+#'              package = "sigminer", mustWork = TRUE))
 #' draw_cn_components(cn_prepare$features, cn_prepare$components)
-#' }
 #' @family copy number plot
 #'
 draw_cn_components = function(features, components, ...) {
@@ -376,17 +360,10 @@ draw_cn_components = function(features, components, ...) {
 #' @import ggplot2
 #' @export
 #' @examples
-#' \donttest{
-#' load(system.file("extdata", "example_cn_list.RData",
-#'      package = "sigminer", mustWork = TRUE))
-#' segTabs = data.table::rbindlist(tcga_segTabs, idcol = "sample")
-#' cn = read_copynumber(segTabs,
-#'                      seg_cols = c("chromosome", "start", "end", "segVal"),
-#'                      genome_build = "hg19")
-#' cn_prepare =  sig_prepare(cn)
-#' res = sig_extract(cn_prepare$nmf_matrix, 3, mode = "copynumber", nrun = 5)
+#' # Load copy number signature
+#' load(system.file("extdata", "toy_copynumber_signature.RData",
+#'              package = "sigminer", mustWork = TRUE))
 #' draw_sig_profile(res$nmfObj)
-#' }
 #' @family signature plot
 draw_sig_profile = function(nmfObj, mode = c("copynumber", "mutation"),
                             y_scale = c("relative", "absolute"), font_scale = 1) {
@@ -481,17 +458,10 @@ draw_sig_profile = function(nmfObj, mode = c("copynumber", "mutation"),
 #' @importFrom grDevices rainbow
 #' @export
 #' @examples
-#' \donttest{
-#' load(system.file("extdata", "example_cn_list.RData",
-#'      package = "sigminer", mustWork = TRUE))
-#' segTabs = data.table::rbindlist(tcga_segTabs, idcol = "sample")
-#' cn = read_copynumber(segTabs,
-#'                      seg_cols = c("chromosome", "start", "end", "segVal"),
-#'                      genome_build = "hg19")
-#' cn_prepare =  sig_prepare(cn)
-#' res = sig_extract(cn_prepare$nmf_matrix, 3, mode = "copynumber", nrun = 5)
+#' # Load copy number signature
+#' load(system.file("extdata", "toy_copynumber_signature.RData",
+#'              package = "sigminer", mustWork = TRUE))
 #' draw_sig_activity(res$nmfObj)
-#' }
 #' @family signature plot
 draw_sig_activity = function(nmfObj, mode = c("copynumber", "mutation"),
                              font_scale = 1, hide_samps = TRUE) {
@@ -574,14 +544,9 @@ draw_sig_activity = function(nmfObj, mode = c("copynumber", "mutation"),
 #' @export
 #' @examples
 #' \donttest{
-#' load(system.file("extdata", "example_cn_list.RData",
-#'      package = "sigminer", mustWork = TRUE))
-#' segTabs = data.table::rbindlist(tcga_segTabs, idcol = "sample")
-#' cn = read_copynumber(segTabs,
-#'                      seg_cols = c("chromosome", "start", "end", "segVal"),
-#'                      genome_build = "hg19")
-#' cn_prepare =  sig_prepare(cn)
-#' res = sig_extract(cn_prepare$nmf_matrix, 3, mode = "copynumber", nrun = 5)
+#' # Load copy number signature
+#' load(system.file("extdata", "toy_copynumber_signature.RData",
+#'              package = "sigminer", mustWork = TRUE))
 #' sig_activity = sig_get_activity(res$nmfObj)
 #' sig_cor = sig_get_correlation(sig_activity)
 #' draw_sig_corrplot(sig_cor)
@@ -622,23 +587,20 @@ draw_sig_corrplot = function(mat_list, order = "original", type = "lower",
 #' @import ggplot2
 #' @export
 #' @examples
-#' \donttest{
-#' load(system.file("extdata", "example_cn_list.RData",
-#'      package = "sigminer", mustWork = TRUE))
-#' segTabs = data.table::rbindlist(tcga_segTabs, idcol = "sample")
-#' cn = read_copynumber(segTabs,
-#'                      seg_cols = c("chromosome", "start", "end", "segVal"),
-#'                      genome_build = "hg19")
-#' cn_prepare =  sig_prepare(cn)
-#' res = sig_extract(cn_prepare$nmf_matrix, 3, mode = "copynumber", nrun = 5)
-#' subtypes = sig_assign_samples(res$nmfObj)
+#' # Load copy number signature
+#' load(system.file("extdata", "toy_copynumber_signature.RData",
+#'              package = "sigminer", mustWork = TRUE))
+#' # Assign samples to clusters
+#' subtypes = sig_assign_samples(res$nmfObj, type = "samples")
+#'
 #' set.seed(1234)
+#' # Add custom groups
 #' subtypes$new_group = sample(c("1", "2","3", "4"), size = nrow(subtypes), replace = TRUE)
+#' # Summarize subtypes
 #' subtypes.sum = sig_summarize_subtypes(subtypes[, -1], col_subtype = "nmf_subtypes",
-#'                                      cols_to_summary = colnames(subtypes[, -1])[-1],
-#'                                      type = c("co", "ca"), verbose = TRUE)
-#' plot_list = draw_subtypes_comparison(subtypes.sum)
-#' }
+#'                          cols_to_summary = colnames(subtypes[, -1])[c(-1,-2)],
+#'                          type = c("co", "ca"), verbose = TRUE)
+#' draw_subtypes_comparison(subtypes.sum)
 #' @family signature plot
 draw_subtypes_comparison = function(subtype_summary,
                                     xlab = "subtype", ylab_co = NA,

diff --git a/R/get_series.R b/R/get_series.R
@@ -35,11 +35,9 @@
 #' @return a `list`
 #' @export
 #' @examples
-#' \donttest{
 #' extdata_dir = system.file("extdata", package = "sigminer", mustWork = TRUE)
 #' cp = read_copynumber(extdata_dir, pattern = "txt", genome_build = "hg19")
 #' cn_list = get_cnlist(cp)
-#' }
 #' @family internal calculation function series
 
 get_cnlist = function(CopyNumber) {
@@ -75,12 +73,10 @@ get_cnlist = function(CopyNumber) {
 #' @import foreach
 #' @export
 #' @examples
-#' \donttest{
-#' extdata_dir = system.file("extdata", package = "sigminer", mustWork = TRUE)
-#' cp = read_copynumber(extdata_dir, pattern = "txt", genome_build = "hg19")
-#' cn_list = get_cnlist(cp)
+#' # Load copy number list
+#' load(system.file("extdata", "toy_cnlist.RData",
+#'              package = "sigminer", mustWork = TRUE))
 #' cn_features = get_features(cn_list, cores = 1)
-#' }
 #' @family internal calculation function series
 
 get_features = function(CN_data,
@@ -179,10 +175,9 @@ get_features = function(CN_data,
 #' @export
 #' @examples
 #' \donttest{
-#' extdata_dir = system.file("extdata", package = "sigminer", mustWork = TRUE)
-#' cp = read_copynumber(extdata_dir, pattern = "txt", genome_build = "hg19")
-#' cn_list = get_cnlist(cp)
-#' cn_features = get_features(cn_list, cores = 1)
+#' # Load copy number features
+#' load(system.file("extdata", "toy_cn_features.RData",
+#'              package = "sigminer", mustWork = TRUE))
 #' cn_components = get_components(cn_features)
 #' }
 #' @family internal calculation function series
@@ -311,14 +306,14 @@ get_components = function(CN_features,
 #' @importFrom utils data download.file str
 #' @export
 #' @examples
-#' \donttest{
-#' extdata_dir = system.file("extdata", package = "sigminer", mustWork = TRUE)
-#' cp = read_copynumber(extdata_dir, pattern = "txt", genome_build = "hg19")
-#' cn_list = get_cnlist(cp)
-#' cn_features = get_features(cn_list, cores = 1)
-#' cn_components = get_components(cn_features)
+#' # Load copy number components
+#' load(system.file("extdata", "toy_cn_components.RData",
+#'              package = "sigminer", mustWork = TRUE))
+#' # Load copy number features
+#' load(system.file("extdata", "toy_cn_features.RData",
+#'              package = "sigminer", mustWork = TRUE))
+#'
 #' cn_matrix = get_matrix(cn_features, cn_components)
-#' }
 #' @family internal calculation function series
 get_matrix = function(CN_features,
                       all_components = NULL,
@@ -393,12 +388,10 @@ get_matrix = function(CN_features,
 #' @return a data table
 #' @export
 #' @examples
-#' \donttest{
-#' extdata_dir = system.file("extdata", package = "sigminer", mustWork = TRUE)
-#' cp = read_copynumber(extdata_dir, pattern = "txt", genome_build = "hg19")
-#' cn_list = get_cnlist(cp)
+#' # Load copy number list
+#' load(system.file("extdata", "toy_cnlist.RData",
+#'              package = "sigminer", mustWork = TRUE))
 #' annot = get_LengthFraction(cn_list, seg_cols = c("chromosome", "start", "end", "segVal"))
-#' }
 #' @family internal calculation function series
 get_LengthFraction = function(CN_data,
                               genome_build = c("hg19", "hg38"),

diff --git a/R/prepare_series.R b/R/prepare_series.R
@@ -21,12 +21,9 @@
 #' @export
 #' @examples
 #' \donttest{
-#' load(system.file("extdata", "example_cn_list.RData",
-#'      package = "sigminer", mustWork = TRUE))
-#' segTabs = data.table::rbindlist(tcga_segTabs, idcol = "sample")
-#' cn = read_copynumber(segTabs,
-#'                      seg_cols = c("chromosome", "start", "end", "segVal"),
-#'                      genome_build = "hg19")
+#' # Load copy number object
+#' load(system.file("extdata", "toy_copynumber.RData",
+#'              package = "sigminer", mustWork = TRUE))
 #' cn_prepare =  prepare_copynumber(cn)
 #' }
 #' @family signature analysis prepare function series

diff --git a/R/read_series.R b/R/read_series.R
@@ -12,7 +12,8 @@
 #' laml.maf = system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
 #' laml = read_maf(maf = laml.maf)
 #' }
-#'
+#' @export
+#' @family read genomic variation data function series
 
 read_maf = function(
   maf, clinicalData = NULL, removeDuplicatedVariants = TRUE,
@@ -68,14 +69,12 @@ read_maf = function(
 #' @return a [CopyNumber] object
 #' @export
 #' @examples
-#' \donttest{
-#' load(system.file("extdata", "example_cn_list.RData",
+#' # Load toy dataset of absolute copynumber profile
+#' load(system.file("extdata", "toy_segTab.RData",
 #'              package = "sigminer", mustWork = TRUE))
-#' segTabs = data.table::rbindlist(tcga_segTabs, idcol = "sample")
 #' cn = read_copynumber(segTabs,
-#'                      seg_cols = c("chromosome", "start", "end", "segVal"),
-#'                                                    genome_build = "hg19")
-#' }
+#'              seg_cols = c("chromosome", "start", "end", "segVal"),
+#'              genome_build = "hg19", complement = FALSE, verbose = TRUE)
 #' @family read genomic variation data function series
 read_copynumber = function(input,
                            pattern = NULL,
@@ -339,6 +338,9 @@ read_copynumber = function(input,
     message("  Filter - ", nrow(dropoff_df))
   }
 
+  # make sure seg value is integer
+  data_df[["segVal"]] = as.integer(round(data_df[["segVal"]]))
+
   if (verbose) message("Anotating...")
   annot = get_LengthFraction(data_df,
                              genome_build = genome_build,
@@ -350,27 +352,16 @@ read_copynumber = function(input,
                                     genome_measure = genome_measure )
 
   if (verbose) message("Done!")
-  if (is.null(clinical_data)) {
-    res = CopyNumber(
-      data =  data_df,
-      summary.per.sample = sum_sample,
-      genome_build = genome_build,
-      genome_measure = genome_measure,
-      annotation = annot,
-      dropoff.segs = dropoff_df,
-      clinical.data = data.table::data.table()
-    )
-  } else {
-    res = CopyNumber(
-      data =  data_df,
-      summary.per.sample = sum_sample,
-      genome_build = genome_build,
-      genome_measure = genome_measure,
-      annotation = annot,
-      dropoff.segs = dropoff_df,
-      clinical.data = data.table::as.data.table(clinical_data)
-    )
-  }
+
+  res = CopyNumber(
+    data =  data_df,
+    summary.per.sample = sum_sample,
+    genome_build = genome_build,
+    genome_measure = genome_measure,
+    annotation = annot,
+    dropoff.segs = dropoff_df,
+    clinical.data = data.table::as.data.table(clinical_data)
+  )
 
   res = validate_segTab(res, verbose = verbose)
   res
@@ -415,20 +406,14 @@ validate_segTab = function(object, verbose = FALSE){
 #' @return a [GenomicVariation] object
 #' @export
 #' @examples
-#' \donttest{
 #' # Read MAF
 #' laml.maf = system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
 #' laml = read_maf(maf = laml.maf)
-#' # Read absolute copy number profile
-#' load(system.file("extdata", "example_cn_list.RData",
+#' # Load copy number object
+#' load(system.file("extdata", "toy_copynumber.RData",
 #'              package = "sigminer", mustWork = TRUE))
-#' segTabs = data.table::rbindlist(tcga_segTabs, idcol = "sample")
-#' cn = read_copynumber(segTabs,
-#'                      seg_cols = c("chromosome", "start", "end", "segVal"),
-#'                                                    genome_build = "hg19")
 #' # Combine as GenomicVariation object
 #' gv = read_variation(cn, laml)
-#' }
 #' @family read genomic variation data function series
 read_variation = function(copynumber, maf, clinical_data = NULL) {