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add getSurvival #112

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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
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0xMuluh Aug 22, 2025
63510e5
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0xMuluh Sep 1, 2025
c7be3ed
Merge branch 'devel' into cox
TuomasBorman Sep 10, 2025
1492bb1
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TuomasBorman Sep 10, 2025
9fc9a92
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TuomasBorman Sep 10, 2025
a33c6d1
add unit tests
0xMuluh Sep 12, 2025
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2 changes: 2 additions & 0 deletions DESCRIPTION
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Expand Up @@ -27,11 +27,13 @@ Depends:
mia
Imports:
dplyr,
glmnet,
methods,
S4Vectors,
SingleCellExperiment,
stats,
SummarizedExperiment,
survival,
tidyr,
TreeSummarizedExperiment
Suggests:
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9 changes: 9 additions & 0 deletions NAMESPACE
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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
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@@ -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)
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10 changes: 10 additions & 0 deletions R/AllGenerics.R
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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"))
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