Skip to content

add getSurvival #112

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
0xMuluh wants to merge 10 commits into
base: devel
Choose a base branch
from
Open

add getSurvival #112

Show file tree
Hide file tree
Changes from 9 commits
Commits
Show all changes
10 commits
Select commit Hold shift + click to select a range
9e30ba3
add getSurvival
0xMuluh May 6, 2025
2b1fead
up
0xMuluh Aug 22, 2025
498b545
Merge branch 'devel' into cox
0xMuluh Aug 22, 2025
38fd536
up
0xMuluh Aug 22, 2025
059f109
up
0xMuluh Aug 22, 2025
63510e5
up
0xMuluh Sep 1, 2025
c7be3ed
Merge branch 'devel' into cox
TuomasBorman Sep 10, 2025
1492bb1
up
TuomasBorman Sep 10, 2025
9fc9a92
up
TuomasBorman Sep 10, 2025
a33c6d1
add unit tests
0xMuluh Sep 12, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions DESCRIPTION
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,11 +27,13 @@ Depends:
mia
Imports:
dplyr,
glmnet,
methods,
S4Vectors,
SingleCellExperiment,
stats,
SummarizedExperiment,
survival,
tidyr,
TreeSummarizedExperiment
Suggests:
Expand Down
9 changes: 9 additions & 0 deletions NAMESPACE
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,21 +5,25 @@ export(addBimodality)
export(addShortTermChange)
export(addStability)
export(addStepwiseDivergence)
export(addSurvival)
export(getBaselineDivergence)
export(getBimodality)
export(getShortTermChange)
export(getStability)
export(getStepwiseDivergence)
export(getSurvival)
exportMethods(addBaselineDivergence)
exportMethods(addBimodality)
exportMethods(addShortTermChange)
exportMethods(addStability)
exportMethods(addStepwiseDivergence)
exportMethods(addSurvival)
exportMethods(getBaselineDivergence)
exportMethods(getBimodality)
exportMethods(getShortTermChange)
exportMethods(getStability)
exportMethods(getStepwiseDivergence)
exportMethods(getSurvival)
import(S4Vectors)
import(SingleCellExperiment)
import(SummarizedExperiment)
Expand All @@ -44,9 +48,14 @@ importFrom(dplyr,summarize)
importFrom(dplyr,sym)
importFrom(dplyr,ungroup)
importFrom(dplyr,vars)
importFrom(glmnet,Cindex)
importFrom(glmnet,cv.glmnet)
importFrom(glmnet,glmnet)
importFrom(stats,coef)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,setNames)
importFrom(survival,Surv)
importFrom(survival,coxph)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,unnest)
3 changes: 3 additions & 0 deletions NEWS
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,6 @@
Changes in version 0.99.11
+ Added wrapper for survival analysis

Changes in version 0.99.10
Date: 2025-09-06
+ Added survival data on Crohn's disease (crohn_survival)
Expand Down
10 changes: 10 additions & 0 deletions R/AllGenerics.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,3 +50,13 @@ setGeneric("getStability", signature = "x", function(x, ...)
#' @export
setGeneric("addStability", signature = "x", function(x, ...)
standardGeneric("addStability"))

#' @rdname getSurvival
#' @export
setGeneric("getSurvival", signature = "x", function(x, ...)
standardGeneric("getSurvival"))

#' @rdname getSurvival
#' @export
setGeneric("addSurvival", signature = "x", function(x, ...)
standardGeneric("addSurvival"))
Loading
Loading