Calculates Kaplan-Meier estimates for genotype specific survival effects
Version | 1.6.1 |
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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 |
Name | Type | Mandatory | Description |
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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 |
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statistics | CSV | Kaplan-Meier statistics for the given markers |
report | Latex | LaTeX-document for the plots and summary. |
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 case | Parameters▼ | IN genotypes |
IN survival |
IN annotations |
OUT statistics |
OUT report |
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case1 | properties | genotypes | survival | (missing) | statistics | report |
timeCol = Ageatlastupdate, |
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case2 | properties | genotypes | survival | annotations | statistics | (missing) |
timeCol = Ageatlastupdate, |
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case3 | properties | genotypes | survival | annotations | statistics | (missing) |
timeCol = Ageatlastupdate, |
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case4 | properties | genotypes | survival | (missing) | (expecting failure) | (expecting failure) |
timeCol = Ageatlastupdate, |
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case5_cox | properties | genotypes | survival | (missing) | statistics | (missing) |
timeCol = Ageatlastupdate, |
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case7_unicox | properties | genotypes | survival | (missing) | statistics | (missing) |
timeCol = Ageatlastupdate, |
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case9_comHom | properties | genotypes | survival | (missing) | statistics | (missing) |
timeCol = Ageatlastupdate, |