processDataMutSurv {cancerGI}

Find matched individuals in mutation and survival data

Description

This functions finds matched individuals in data.mut and data.surv, and outputs the two data sets with only matched individuals.

Usage

processDataMutSurv(data.mut, data.surv, colTime = 2, colStatus = 3)

Arguments

data.mut

Integer matrix of genes by cases. The first column contains gene names. Each of the other columns contains mutation patterns of a case: 0 as wildtype, 1 amplification and -1 deletion.

data.surv

Data frame containing case ID, survival time and survival status. Cases do not need to match those in data.mut.

colTime

Scalar indicating which column in data.surv contains the survival time.

colStatus

A character string indicating which column in data.surv contains the survival status: "DECEASED" or "LIVING".

Value

A list of two data frames, data.mut and data.surv. Format of the data frames is the same as input, except that the individuals in the two data frames are matched.

Author(s)

Audrey Q. Fu, Xiaoyue Wang

References

Wang, X., Fu, A. Q., McNerney, M. and White, K. P. (2014). Widespread genetic epistasis among breast cancer genes. Nature Communications. 5 4828. doi: 10.1038/ncomms5828

See Also

computeSurvivalPValueForGenePairSet.output