LCox: Hypothesis Testing for longitudinal gene profiles and the...

In LCox: A Tool for Selecting Genes Related to Survival Outcomes using Longitudinal Gene Expression Data

Description

LCox is a function that performs hypothesis tests of the associations between longitudinal gene profiles and the survival outcome.

Usage

LCox(data = NULL, data.id = NULL, geneID = 3:4, varID = NULL,
  PLOT = FALSE, optns = list(dataType = "Sparse", FVEthreshold = 0.95,
  methodBwMu = "CV"))

Arguments

data	A data frame contains longitudinal gene expression data. This data frame must contain a column of ID to identify each patient and a column of years to indicate the follow-up time for each data point.
data.id	A data frame contains the survival outcome and important covariates. This data frame must contain a column of ID to identify each patient, a column of fstat to indicate the censoring time, and a column of ftime to indicate the survival time.
geneID	A vector of integers indicates the column numbers in data for the genes of interest.
varID	A vector of integers indicates the column numbers in data.id for the important confounding covariates that need to be included.
PLOT	A logical value indicates whether a graph showing the fitted lines is desired. If TRUE, a figure "fitted.pdf" will be saved to the current working directory.
optns	A list of options control parameters for the FPCA model.

Value

returns a matrix with one column being the p values and the other column being the number of eigenfunctions (K).

References

LCox: A tool for selecting genes related to survival outcomes using longitudinal gene expression data. Jiehuan Sun, Jose D. Herazo-Maya, Jane-Ling Wang, Naftali Kaminski, and Hongyu Zhao.

Examples

data.list = simudata()
data = data.list$data
data.id = data.list$data.id
res = LCox(data = data, data.id = data.id, geneID = 3:4)
res = LCox(data = data, data.id = data.id, geneID = 3:4, varID = 4)
res = LCox(data = data, data.id = data.id, geneID = 3:4, PLOT=TRUE)

LCox documentation built on May 2, 2019, 8:32 a.m.