signatureExp {signatureSurvival}

Signature expression or signature score

Description

Function signatureExp.R is used to give signature expression or score across all patients in a cohort data by using weight vector of a signature.

Usage

signatureExp(svdata,weight)

Arguments

svdata

a survival dataset containing clinic data such as death or relapse status, month, covariates age, sex and/smoking, stages, therapy etc. and a set of genes containing subset of genes in the signature in column.

weight

a matrix that contains gene and/or gene_id and weight columns.

Details

a matrix with g \times (2 or 3). If weight contains two columns, then first column must be gene or gene_id and the second column must be weight. If weight has three columns, then the first two columns are gene and gene_id but the third column must be weight. Gene name or gene_id in weigth must be matched with gene name or gene_id in the survival data.

Value

a survival dataset with signature scores of patients.

Author(s)

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

See Also

weight

Examples

data(TCGA_survivalData)
data(signature_weight)
res1<-signatureExp(svdata=TCGA_survivalData,weight=signature_weight)