Component: SNPKaplanMeier

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 SNPKaplanMeier( genotypes = SNPMatrix, survival = CSV, //annotations = AnnotationTable, PLimit = 1.00, censoring = "right", combineCommonHom = false, confInt = 0.95, minCount = 0, minFreq = 0.01, modelVars = "genotype", naLimit = 0.1, nullCalls = "", outputAllPValues = false, sampleCol = <string>, showCI = false, skipMissingGT = false, statusCol = <string>, strictLimits = false, survRatePoint = 0.5, timeCol = <string>, timeCol2 = "", timeOutLimit = -1, timeStartCol = "", title = "Genotype Specific Survival Estimates", useCox = false )

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.

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.

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

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.

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

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,

Test case

Parameters▼

IN
genotypes

IN
survival

IN
annotations

OUT
statistics

OUT
report

case1

(missing)

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

case2

(missing)

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

case3

(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)

case5_cox

(missing)

(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

(missing)

(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

(missing)

(missing)

Anduril

SNPKaplanMeier

Inputs

Outputs

Parameters

Test cases