Up: Component summary Component

SNPKaplanMeier

Calculates Kaplan-Meier estimates for genotype specific survival effects

Version 1.6.1
Bundle microarray
Categories SNP Latex Survival
Authors Marko Laakso (Marko.Laakso@Helsinki.FI), Riku Louhimo (Riku.Louhimo@Helsinki.FI)
Issue tracker View/Report issues
Requires rms (R-package)
Source files component.xml SNPKaplanMeier.r
Usage Example with default values

Inputs

Name Type Mandatory Description
genotypes SNPMatrix Mandatory Genotype calls
survival CSV Mandatory Survival time and event indicator
annotations AnnotationTable Optional Additional information about the markers. This data will be shown on the report of interesting markers.

Outputs

Name Type Description
statistics CSV Kaplan-Meier statistics for the given markers
report Latex LaTeX-document for the plots and summary.

Parameters

Name Type Default Description
PLimit float 1.00 Ignore results with a p-value greater than this limit. If 'useCox=true' then the limit is defined by the minimum p-value of the two possible.
censoring string "right" Choose censoring type. One of 'right' (default), 'left', 'counting', 'interval' or 'interval2'.
combineCommonHom boolean false Combine common homozygotes with heterozygotes in all markers.
confInt float 0.95 Coverage of the confidence intervals [0,1]
minCount int 0 Combine rare (aa) homozygotes to heterozygotes (Aa) if their number is below this limit. This parameter is used together with minFreq so that the actual limit is max(minFreq*n, minCount).
minFreq float 0.01 Combine rare (aa) homozygotes to heterozygotes (Aa) if their frequency is below this limit. See also minCount.
modelVars string "genotype" A comma separated list of co-variates used in Cox regression. Only the first value is is used if useCox=false.
naLimit float 0.1 Skip markers where one minus call rate exceeds this limit.
nullCalls string "" A comma separated list of genotype calls that will be considered as missing values
outputAllPValues boolean false Print all p-values in output even if insignificant. SNPs with insignificant p-values will not have survival curves, however.
sampleCol string (no default) Column name for the sample name
showCI boolean false Draw confidence intervals to the graph
skipMissingGT boolean false Simply skip those samples that lack the genotype information.
statusCol string (no default) Column name for the event indicator
strictLimits boolean false Skip marker if the combined count or frequency of rare homozygote and heterozygote is below max(minFreq*n, minCount). See also minCount and minFreq.
survRatePoint float 0.5 Sampling height for the distances between the survival expectations. Negative values may be used to suppress these measurements.
timeCol string (no default) Column name for the survival time
timeCol2 string "" Column name for stydy entry time for left-truncation. Study times are assumed to yield correct left-truncation form with timeCol+timeCol2. Only works if useCox=true.
timeOutLimit float -1 Cut survival curves after this limit. A negative value can be used to maximize the length of the period.
timeStartCol string "" Column name for the start time that is reduced from the survival time. Default (empty) does not subtract anything.
title string "Genotype Specific Survival Estimates" Section title
useCox boolean false Utilize Cox regression.

Test cases

Test case Parameters IN
genotypes
IN
survival
IN
annotations
OUT
statistics
OUT
report
case1 properties genotypes survival (missing) statistics report

timeCol = Ageatlastupdate,
timeStartCol = Dgage,
statusCol = Vitalstatus,
sampleCol = ID,
minFreq = 0.05,
skipMissingGT = true,
showCI = true,
nullCalls = --

case2 properties genotypes survival annotations statistics (missing)

timeCol = Ageatlastupdate,
timeStartCol = Dgage,
statusCol = Vitalstatus,
sampleCol = ID,
minFreq = 0.05,
skipMissingGT = true,
nullCalls = --

case3 properties genotypes survival annotations statistics (missing)

timeCol = Ageatlastupdate,
statusCol = Vitalstatus,
sampleCol = ID,
minFreq = 0.05,
skipMissingGT = true,
showCI = true,
nullCalls = --,
timeOutLimit = 120,
survRatePoint = 0.7

case4 properties genotypes survival (missing) (expecting failure) (expecting failure)

timeCol = Ageatlastupdate,
timeStartCol = Dgage,
statusCol = Vitalstatus,
sampleCol = ID,
minFreq = 0.05,
skipMissingGT = true,
showCI = true,
nullCalls = --,
timeOutLimit = 120

case5_cox properties genotypes survival (missing) statistics (missing)

timeCol = Ageatlastupdate,
timeStartCol = Dgage,
statusCol = Vitalstatus,
sampleCol = ID,
minFreq = 0.05,
skipMissingGT = true,
showCI = true,
nullCalls = --,
useCox = true,
modelVars = genotype,Dgage,
title = "Genotype specific survival estimates with cox regression computed CIs",
PLimit = 0.7,
confInt = 0.90,
naLimit = 0.2,
outputAllPValues = true

case7_unicox properties genotypes survival (missing) statistics (missing)

timeCol = Ageatlastupdate,
timeStartCol = Dgage,
statusCol = Vitalstatus,
sampleCol = ID,
minFreq = 0.05,
skipMissingGT = true,
showCI = true,
nullCalls = --,
useCox = true,
modelVars = genotype,
title = "Genotype specific survival estimates with cox regression computed CIs",
PLimit = 0.7,
confInt = 0.90,
naLimit = 0.2,
outputAllPValues = true

case9_comHom properties genotypes survival (missing) statistics (missing)

timeCol = Ageatlastupdate,
timeStartCol = Dgage,
statusCol = Vitalstatus,
sampleCol = ID,
minFreq = 0.05,
skipMissingGT = true,
showCI = true,
nullCalls = --,
combineCommonHom = true,


Generated 2018-12-12 07:42:05 by Anduril 2.0.0