MVKMresult {signatureSurvival}

Multivariate survival analysis with multiple specified independent variables

Description

Function MVKMresult performs multivariate Cox proportional hazard survival analysis with a set of patients and an independent variable (a specified gene or a feature) and a set of covariates (age, sex and/or smoking or stage) and outputs hazard risks (HR), z-scores, and p-values of the gene and these covariates.

Usage

MVKMresult(data,X,mol, status="status",time="month",quant=c("No",-0.2,0.2))

Arguments

data

survival data containing p patients in row, s survival variables such as survival status for death, recurrence or relapse, survival time such as day, month,or year, covariates age, sex and/or smoking, etc. and a set of genes in column.

X

string for covariate(s), number of covariates is limited to 10. If X=NULL, then MVKMresult would be stopped.

mol

int value for column number of the first gene specified.

status

string for survival status of patients, may be "relapse" or "recurrence" or "death". User can set status="death", "relapse" or "recurrence","status" depending on user's survival data. The default value is "status".

time

string for survival time and may be one of c("day", "month", "year"), depending on the clinical data. The default value is "month".

quant

vector for quantile, low and high values. the low and high values are used to define or classify low and high expression groups. If quantile is "yes" or "YES", then the low and high are non-negative precent values, for example, quant=c("yes",0.25,0.75). If quantile is "no", then the low and high values are z-scores, the low value may be negative. For example, quant=c("no",-0.2, 0.2). The quantile = "yes" or = "No" may produce different results of survival analysis. User should carefully choose quantile or no quantile according to the data. The default values are c("no",-0.2,0.2).

Details

Function MVKMresult performs multivariate Cox proportional hazard survival analyses with p patients and a specified gene and a set of covariates specified and outputs hazard risk (HR),z-score and p-value for the specified gene or signature and covariates.

Value

output a matrix with one row and multiple columns for gene name, Hazard risk, hazard rate, standard error, z-value, p-value of gene and covariates.

Note

User can also use SKMCresult to screen a prognostic signature and a weight vector without covariates.

All inputting parameters are not sensitive to upper or lower. That is, user can input upper or lower string or letter. For example, both time ="MONTH" or time = "month" work.

Author(s)

Yuan-De Tan
[e-mail]
[e-mail]
Yuguang Ban
[e-mail]

See Also

SKMCresult,musvtest,mvstest

Examples

data(GSE50081)
res<-MVKMresult(data=GSE50081,X=c("t.stage","n.stage","m.stage"),mol=3500,
status="status",time="month",quant=c("no",-0.2,0.2))