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KaplanMeier

Produces a Kaplan-Meier plot representing survival estimates based on the given data.

This is a simple example output.

Version 2.2
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Categories Survival Latex
Authors Marko Laakso (Marko.Laakso@Helsinki.FI), Riku Louhimo (Riku.Louhimo@Helsinki.FI), Kristian Ovaska (kristian.ovaska@helsinki.fi), Ali Faisal (ali.faisal@aalto.fi)
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Requires survival (R-package)
Source files component.xml KaplanMeier.r
Usage Example with default values

Inputs

Name Type Mandatory Description
survival CSV Mandatory Survival time and event indicators, and the sample group assignments.
annotation AnnotationTable Optional Additional annotations for the groupCol names. These annotations are listed as column name value pairs in figure caption.

Outputs

Name Type Description
report Latex LaTeX-document for the plots and summary
statistics CSV Kaplan-Meier statistics for the sample groups. All plotted groups are present; in addition, groups for which the p-value is above PLimit are present in this table but they are not plotted. This table contains also file names of the document figures. If a group was not plotted, the file name is NA.
plots Array<PDF> An array of the Kaplan-Meier curves that are also part of the report

Parameters

Name Type Default Description
PLimit float 1.00 Ignore results with a p-value greater than this limit
annotCol string "*" A comma separated list of column names of the annotation file that will be shown in the report. An asterisk (*) may be used for all attributes except the first one that is considered as a key.
confInt float 0.95 Coverage of the confidence intervals [0,1] or a negative number to disable them
contiCols string "" A comma separated list of column names that contain continuous variables (e.g., age). By default columns are assumed to contain categories.
eventSymbol string "1" Value of statusCol column indicating an event. Other values are considered as censorings.
excludeCol string "" A comma separated list of column names that should not be used as groupCols even if an asterisk is used. This is especially useful to filter out samples identifiers and other irrelevant columns.
groupCol string "" A comma separated list of column names of sample group identifiers or an empty string for a single curve. An asterisk (*) may be used to plot all attributes except those defined for the other purposes or listed in excludeCol.
minCount int 0 Individual groups with less that this many members will be left out
minGroups int 0 No results are produced for the sets where the analysis (after the minCount pruning) consists of less than this many groups
modelVarCols string "" Comma separated list of column names for background variables in the Cox model. Default indicates that only the logrank test is used for p-value computation. If columns are defined here, the PLimit parameter refers to the Cox p-values.
printTable boolean false Print table of number of risk individuals in seven even intervals.
statusCol string (no default) Column name for the event indicator
strataCols string "" Comma separated list of column names for background variables that should be stratified in the Cox model.
timeCol string (no default) Column name for the survival time
timeOutLimit float -1 Cut survival curves after this limit. A negative value can be used to maximize the length of the period.
title string "Kaplan-Meier survival estimates" Figure title
xLabel string "survival time" Label for the horizontal time axis

Test cases

Test case Parameters IN
survival
IN
annotation
OUT
report
OUT
statistics
OUT
plots
case1 properties survival (missing) report statistics plots

timeCol = Followup,
statusCol = Vitalstatus,
groupCol = SNP_Add_Uncommon,
minCount = 60,
timeOutLimit = 30

case2_one_group properties survival annotation report statistics plots

timeCol = Followup,
statusCol = Vitalstatus,
confInt = -1,
annotCol = showMe

case3_multiple_plots properties survival annotation report statistics plots

timeCol = Followup,
statusCol = Vitalstatus,
groupCol = *,
excludeCol = ID,Dgage,Ageatlastupdate,Foll_20y,Death_20y

case4_plimit properties survival (missing) report statistics plots

timeCol = Followup,
statusCol = Vitalstatus,
groupCol = *,
excludeCol = ID,
PLimit = 0.5,
eventSymbol = 0,
title = Kaplan-Meier test,
xLabel = Ueberlebensdauer

case5_cox properties survival (missing) (missing) statistics plots

excludeCol = PatientID,time,status,gender,race,age,
statusCol = status,
timeCol = time,
groupCol = *,
modelVarCols = gender,race,age,
contiCols = age,
PLimit = 0.75

case6_strata properties survival (missing) (missing) statistics (missing)

excludeCol = PatientID,time,status,gender,race,age,
statusCol = status,
timeCol = time,
groupCol = *,
modelVarCols = ,
strataCols = gender,
PLimit = 0.75

case7_confInt properties survival (missing) (missing) (missing) (missing)

statusCol=Event,
timeCol=Time,
groupCol=Group,
confInt=-1


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