| ... | ... |
@@ -2,7 +2,7 @@ Package: omada |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Machine learning tools for automated transcriptome |
| 4 | 4 |
clustering analysis |
| 5 |
-Version: 1.5.5 |
|
| 5 |
+Version: 1.5.7 |
|
| 6 | 6 |
Authors@R: person("Sokratis", "Kariotis", role = c("aut", "cre"),
|
| 7 | 7 |
email = "[email protected]", |
| 8 | 8 |
comment = c(ORCID = "0000-0001-9993-6017")) |
| ... | ... |
@@ -9,7 +9,6 @@ S3method(get_cluster_voting_k_votes,clusterAnalysis) |
| 9 | 9 |
S3method(get_cluster_voting_memberships,clusterAnalysis) |
| 10 | 10 |
S3method(get_cluster_voting_metric_votes,clusterAnalysis) |
| 11 | 11 |
S3method(get_cluster_voting_scores,clusterAnalysis) |
| 12 |
-S3method(get_coefficient_dataset,geneSignature) |
|
| 13 | 12 |
S3method(get_feature_selection_optimal_features,clusterAnalysis) |
| 14 | 13 |
S3method(get_feature_selection_optimal_number_of_features,clusterAnalysis) |
| 15 | 14 |
S3method(get_feature_selection_scores,clusterAnalysis) |
| ... | ... |
@@ -46,7 +45,6 @@ export(get_cluster_voting_k_votes) |
| 46 | 45 |
export(get_cluster_voting_memberships) |
| 47 | 46 |
export(get_cluster_voting_metric_votes) |
| 48 | 47 |
export(get_cluster_voting_scores) |
| 49 |
-export(get_coefficient_dataset) |
|
| 50 | 48 |
export(get_feature_selection_optimal_features) |
| 51 | 49 |
export(get_feature_selection_optimal_number_of_features) |
| 52 | 50 |
export(get_feature_selection_scores) |
| 53 | 51 |
deleted file mode 100644 |
| ... | ... |
@@ -1,15 +0,0 @@ |
| 1 |
-#' Get a list of LASSO (regression analysis) coefficients of each gene |
|
| 2 |
-#' |
|
| 3 |
-#' @param object An object of class "geneSignature" |
|
| 4 |
-#' @return A list of LASSO (regression analysis) coefficients of each gene |
|
| 5 |
-#' @export |
|
| 6 |
-#' |
|
| 7 |
-#' @examples |
|
| 8 |
- |
|
| 9 |
-get_coefficient_dataset <- function(object) {
|
|
| 10 |
- UseMethod("get_coefficient_dataset")
|
|
| 11 |
-} |
|
| 12 |
-#' @export |
|
| 13 |
-get_coefficient_dataset.geneSignature <- function(object) {
|
|
| 14 |
- object$coefficient.dataset |
|
| 15 |
-} |
| 16 | 0 |
deleted file mode 100644 |
| ... | ... |
@@ -1,17 +0,0 @@ |
| 1 |
-% Generated by roxygen2: do not edit by hand |
|
| 2 |
-% Please edit documentation in R/get_coefficient_dataset.R |
|
| 3 |
-\name{get_coefficient_dataset}
|
|
| 4 |
-\alias{get_coefficient_dataset}
|
|
| 5 |
-\title{Get a list of LASSO (regression analysis) coefficients of each gene}
|
|
| 6 |
-\usage{
|
|
| 7 |
-get_coefficient_dataset(object) |
|
| 8 |
-} |
|
| 9 |
-\arguments{
|
|
| 10 |
-\item{object}{An object of class "geneSignature"}
|
|
| 11 |
-} |
|
| 12 |
-\value{
|
|
| 13 |
-A list of LASSO (regression analysis) coefficients of each gene |
|
| 14 |
-} |
|
| 15 |
-\description{
|
|
| 16 |
-Get a list of LASSO (regression analysis) coefficients of each gene |
|
| 17 |
-} |
| ... | ... |
@@ -68,13 +68,11 @@ cv.memberships <- get_cluster_voting_memberships(omada.analysis) |
| 68 | 68 |
cv.metrics.votes <- get_cluster_voting_metric_votes(omada.analysis) |
| 69 | 69 |
cv.k.votes <- get_cluster_voting_k_votes(omada.analysis) |
| 70 | 70 |
sample.memberships <- get_sample_memberships(omada.analysis) |
| 71 |
-#sf.coefs <- get_signature_feature_coefs(omada.analysis) |
|
| 72 | 71 |
|
| 73 | 72 |
# Plot results |
| 74 | 73 |
plot_partition_agreement(omada.analysis) |
| 75 | 74 |
plot_feature_selection(omada.analysis) |
| 76 | 75 |
plot_cluster_voting(omada.analysis) |
| 77 |
-#plot_signature_feature(omada.analysis) |
|
| 78 | 76 |
``` |
| 79 | 77 |
|
| 80 | 78 |
### Selecting the most appropriate clustering approach based on a dataset |
