SKMCresult {signatureSurvival}

Univariate Cox proportional hazard survival analysis with a specified independent variable

Description

Function SKMCresult performs univariate Cox proportional hazard survival analysis of patients with a specified independent variable or a gene without covariates and outputs hazard risk (HR), z-score, and p-value of this specified gene.

Usage

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

Arguments

data

survival and gene-expression data containing patients in row, survival status for death, recurrence or relapse, survival time and a set of genes in column.

mol

char value specified a gene symbol or a gene id or a signature existed in data or int value for a column number of a specified gene or a signature in data.

time

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

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".

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

Patient survival status is binary variable with 1 for event (such as death) and 0 for no event(such as alive). Genes have expression values(numeric values), which are used to calculate z-scores for classifying patients into two groups: high-expression patients and low-expression patients. SKMCresult performs univariate Cox proportional hazard survival analyses of patients with expression values of a specified gene and outputs hazard risk (HR), z-score and p-value of this specified gene.

Value

output a matrix with one row and 6 columns for gene name, Hazard risk, hazard rate, standard error, z-value, p-value of the specified gene.

Note

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

MVKMresult,musvtest,mvstest

Examples

data(GSE50081)
res<-SKMCresult(data=GSE50081,mol=350, time="month", status="status")