| ... | ... |
@@ -9,7 +9,8 @@ |
| 9 | 9 |
#' @param paired Logical. Indicates if the data is paired or not. Default is FALSE. |
| 10 | 10 |
#' @param var_equal Logical. Indicates if the data variances are assumed to be equal or not. Default is FALSE. |
| 11 | 11 |
#' @param adjust Character. Multiple comparisons correction method to adjust p-values. Available options are: "fdr" (false discovery rate), "holm", "hochberg", "hommel", "bonferroni", "BH" (Benjamini-Hochberg), and "BY" (Benjamini-Yekutieli). |
| 12 |
-#' |
|
| 12 |
+#' @param run_post_hoc Logical. Indicates if computing post-hoc tests or not. Setting this parameter to FALSE can save time for large datasets. |
|
| 13 |
+#' |
|
| 13 | 14 |
#' @export |
| 14 | 15 |
#' |
| 15 | 16 |
#' @return A `list` with the results. |
| ... | ... |
@@ -51,7 +52,8 @@ PomaUnivariate <- function(data, |
| 51 | 52 |
covs = NULL, |
| 52 | 53 |
paired = FALSE, |
| 53 | 54 |
var_equal = FALSE, |
| 54 |
- adjust = "fdr"){
|
|
| 55 |
+ adjust = "fdr", |
|
| 56 |
+ run_post_hoc = TRUE){
|
|
| 55 | 57 |
|
| 56 | 58 |
if(!is(data, "SummarizedExperiment")){
|
| 57 | 59 |
stop("data is not a SummarizedExperiment object. \nSee POMA::PomaCreateObject or SummarizedExperiment::SummarizedExperiment")
|
| ... | ... |
@@ -133,15 +135,19 @@ PomaUnivariate <- function(data, |
| 133 | 135 |
dplyr::as_tibble() |
| 134 | 136 |
|
| 135 | 137 |
# Post-hoc tests |
| 136 |
- post_hoc_tests <- list() |
|
| 137 |
- for (i in 1:nrow(SummarizedExperiment::assay(data))) {
|
|
| 138 |
- post_hoc_tests[[i]] <- dplyr::tibble(feature = rownames(SummarizedExperiment::assay(data))[i], |
|
| 139 |
- broom::tidy(TukeyHSD(aov(to_univariate[,i] ~ group_factor)))[,c(2, 7)]) |
|
| 138 |
+ if (run_post_hoc) {
|
|
| 139 |
+ post_hoc_tests <- list() |
|
| 140 |
+ for (i in 1:nrow(SummarizedExperiment::assay(data))) {
|
|
| 141 |
+ post_hoc_tests[[i]] <- dplyr::tibble(feature = rownames(SummarizedExperiment::assay(data))[i], |
|
| 142 |
+ broom::tidy(TukeyHSD(aov(to_univariate[,i] ~ group_factor)))[,c(2, 7)]) |
|
| 143 |
+ } |
|
| 144 |
+ |
|
| 145 |
+ post_hoc_tests <- dplyr::bind_rows(post_hoc_tests) %>% |
|
| 146 |
+ dplyr::rename(adj_pvalue = adj.p.value) %>% |
|
| 147 |
+ dplyr::arrange(adj_pvalue) |
|
| 148 |
+ } else {
|
|
| 149 |
+ post_hoc_tests <- NULL |
|
| 140 | 150 |
} |
| 141 |
- |
|
| 142 |
- post_hoc_tests <- dplyr::bind_rows(post_hoc_tests) %>% |
|
| 143 |
- dplyr::rename(adj_pvalue = adj.p.value) %>% |
|
| 144 |
- dplyr::arrange(adj_pvalue) |
|
| 145 | 151 |
|
| 146 | 152 |
return(list(result = res_aov, |
| 147 | 153 |
post_hoc_tests = post_hoc_tests)) |
| ... | ... |
@@ -174,20 +180,24 @@ PomaUnivariate <- function(data, |
| 174 | 180 |
dplyr::as_tibble() |
| 175 | 181 |
|
| 176 | 182 |
# Post-hoc tests |
| 177 |
- post_hoc_tests <- list() |
|
| 178 |
- for (i in 1:nrow(SummarizedExperiment::assay(data))) {
|
|
| 179 |
- post_hoc_tests[[i]] <- dplyr::tibble(feature = rownames(SummarizedExperiment::assay(data))[i], |
|
| 180 |
- as.data.frame(TukeyHSD( |
|
| 181 |
- aov(as.formula(paste(colnames(covariates_feat)[1], "~", model_names)), |
|
| 182 |
- data = covariates_feat))$group_factor) %>% |
|
| 183 |
- tibble::rownames_to_column("contrast") %>%
|
|
| 184 |
- dplyr::select(contrast, adj_pvalue = `p adj`) |
|
| 185 |
- ) |
|
| 183 |
+ if (run_post_hoc) {
|
|
| 184 |
+ post_hoc_tests <- list() |
|
| 185 |
+ for (i in 1:nrow(SummarizedExperiment::assay(data))) {
|
|
| 186 |
+ post_hoc_tests[[i]] <- dplyr::tibble(feature = rownames(SummarizedExperiment::assay(data))[i], |
|
| 187 |
+ as.data.frame(TukeyHSD( |
|
| 188 |
+ aov(as.formula(paste(colnames(covariates_feat)[1], "~", model_names)), |
|
| 189 |
+ data = covariates_feat))$group_factor) %>% |
|
| 190 |
+ tibble::rownames_to_column("contrast") %>%
|
|
| 191 |
+ dplyr::select(contrast, adj_pvalue = `p adj`) |
|
| 192 |
+ ) |
|
| 193 |
+ } |
|
| 194 |
+ |
|
| 195 |
+ post_hoc_tests <- dplyr::bind_rows(post_hoc_tests) %>% |
|
| 196 |
+ dplyr::arrange(adj_pvalue) |
|
| 197 |
+ } else {
|
|
| 198 |
+ post_hoc_tests <- NULL |
|
| 186 | 199 |
} |
| 187 | 200 |
|
| 188 |
- post_hoc_tests <- dplyr::bind_rows(post_hoc_tests) %>% |
|
| 189 |
- dplyr::arrange(adj_pvalue) |
|
| 190 |
- |
|
| 191 | 201 |
return(list(result = res_aov_cov, |
| 192 | 202 |
post_hoc_tests = post_hoc_tests)) |
| 193 | 203 |
} |
| ... | ... |
@@ -226,19 +236,23 @@ PomaUnivariate <- function(data, |
| 226 | 236 |
dplyr::as_tibble() |
| 227 | 237 |
|
| 228 | 238 |
# Post-hoc tests |
| 229 |
- post_hoc_tests <- list() |
|
| 230 |
- for (i in 1:nrow(SummarizedExperiment::assay(data))) {
|
|
| 231 |
- post_hoc_tests[[i]] <- dplyr::tibble(feature = rownames(SummarizedExperiment::assay(data))[i], |
|
| 232 |
- FSA::dunnTest(to_univariate[,i] ~ group_factor, |
|
| 233 |
- data = as.data.frame(to_univariate))$res |
|
| 234 |
- ) |
|
| 239 |
+ if (run_post_hoc) {
|
|
| 240 |
+ post_hoc_tests <- list() |
|
| 241 |
+ for (i in 1:nrow(SummarizedExperiment::assay(data))) {
|
|
| 242 |
+ post_hoc_tests[[i]] <- dplyr::tibble(feature = rownames(SummarizedExperiment::assay(data))[i], |
|
| 243 |
+ FSA::dunnTest(to_univariate[,i] ~ group_factor, |
|
| 244 |
+ data = as.data.frame(to_univariate))$res |
|
| 245 |
+ ) |
|
| 246 |
+ } |
|
| 247 |
+ |
|
| 248 |
+ post_hoc_tests <- dplyr::bind_rows(post_hoc_tests) %>% |
|
| 249 |
+ dplyr::select(feature, contrast = Comparison, adj_pvalue = P.adj) %>% |
|
| 250 |
+ dplyr::mutate(contrast = gsub(" ", "", contrast)) %>%
|
|
| 251 |
+ dplyr::arrange(adj_pvalue) |
|
| 252 |
+ } else {
|
|
| 253 |
+ post_hoc_tests <- NULL |
|
| 235 | 254 |
} |
| 236 | 255 |
|
| 237 |
- post_hoc_tests <- dplyr::bind_rows(post_hoc_tests) %>% |
|
| 238 |
- dplyr::select(feature, contrast = Comparison, adj_pvalue = P.adj) %>% |
|
| 239 |
- dplyr::mutate(contrast = gsub(" ", "", contrast)) %>%
|
|
| 240 |
- dplyr::arrange(adj_pvalue) |
|
| 241 |
- |
|
| 242 | 256 |
return(list(result = res_kruskal, |
| 243 | 257 |
post_hoc_tests = post_hoc_tests)) |
| 244 | 258 |
} |
| ... | ... |
@@ -16,7 +16,7 @@ output: github_document |
| 16 | 16 |
| _BioC_ branch | Status | Version | Dependencies | Rank | |
| 17 | 17 |
|- |- |- |- |- | |
| 18 | 18 |
| [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [](https://www.bioconductor.org/packages/POMA) | [](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) | [](https://bioconductor.org/packages/stats/bioc/POMA) | |
| 19 |
-| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [](https://bioconductor.org/packages/stats/bioc/POMA) | |
|
| 19 |
+| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [](https://bioconductor.org/packages/stats/bioc/POMA) | |
|
| 20 | 20 |
|
| 21 | 21 |
<!-- badges: end --> |
| 22 | 22 |
|
| ... | ... |
@@ -18,7 +18,7 @@ v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/li |
| 18 | 18 |
| *BioC* branch | Status | Version | Dependencies | Rank | |
| 19 | 19 |
|-------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------| |
| 20 | 20 |
| [Release](http://bioconductor.org/packages/release/bioc/html/POMA.html) | [](https://bioconductor.org/checkResults/release/bioc-LATEST/POMA/) | [](https://www.bioconductor.org/packages/POMA) | [](http://bioconductor.org/packages/release/bioc/html/POMA.html#since) | [](https://bioconductor.org/packages/stats/bioc/POMA) | |
| 21 |
-| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [](https://bioconductor.org/packages/stats/bioc/POMA) | |
|
| 21 |
+| [Devel](http://bioconductor.org/packages/devel/bioc/html/POMA.html) | [](https://bioconductor.org/checkResults/devel/bioc-LATEST/POMA/) | [](https://bioconductor.org/packages/devel/bioc/html/POMA.html) | [](http://bioconductor.org/packages/devel/bioc/html/POMA.html#since) | [](https://bioconductor.org/packages/stats/bioc/POMA) | |
|
| 22 | 22 |
|
| 23 | 23 |
<!-- badges: end --> |
| 24 | 24 |
|
| ... | ... |
@@ -10,7 +10,8 @@ PomaUnivariate( |
| 10 | 10 |
covs = NULL, |
| 11 | 11 |
paired = FALSE, |
| 12 | 12 |
var_equal = FALSE, |
| 13 |
- adjust = "fdr" |
|
| 13 |
+ adjust = "fdr", |
|
| 14 |
+ run_post_hoc = TRUE |
|
| 14 | 15 |
) |
| 15 | 16 |
} |
| 16 | 17 |
\arguments{
|
| ... | ... |
@@ -25,6 +26,8 @@ PomaUnivariate( |
| 25 | 26 |
\item{var_equal}{Logical. Indicates if the data variances are assumed to be equal or not. Default is FALSE.}
|
| 26 | 27 |
|
| 27 | 28 |
\item{adjust}{Character. Multiple comparisons correction method to adjust p-values. Available options are: "fdr" (false discovery rate), "holm", "hochberg", "hommel", "bonferroni", "BH" (Benjamini-Hochberg), and "BY" (Benjamini-Yekutieli).}
|
| 29 |
+ |
|
| 30 |
+\item{run_post_hoc}{Logical. Indicates if computing post-hoc tests or not. Setting this parameter to FALSE can save time for large datasets.}
|
|
| 28 | 31 |
} |
| 29 | 32 |
\value{
|
| 30 | 33 |
A \code{list} with the results.
|
