aCGH (version 1.50.0)

aCGH.test: Testing association of aCGH clones with censored or continuous outcomes

Description

aCGH.test function tests for association of each clone in an univariate manner with censored or continous outcome by fitting Cox proportional hazards model or linear regression model. There is also an alternative to Cox prop. hazards - testing for differences in survival curves defined by the groups in the outcome variable using the $G^\rho$ family of tests.

Usage

aCGH.test(aCGH.obj, rsp, test = c("survdiff","coxph", "linear.regression"), p.adjust.method = "fdr",imputed=TRUE,  subset = NULL, strt = NULL, ...)

Arguments

aCGH.obj

aCGH object containing clones' log2 ratios.

rsp

Response variable which is either Surv object from survival package or continous outcome.

test

Currently only three values are allowed - "coxph", "survdiff", and "linear.regression", which test for association using Cox proportional hazards model, $G^\rho$ family of tests (survdiff) or linear model.

p.adjust.method

This is a parameter controlling how the p-values from the univariate tests are going to be adjusted for multiple testing. Default value is Benjamini & Hochberg (1995) FDR method. Please refer to p.adjust function for more help.

imputed

Whether imputed or original log2ratios should be used. Default is TRUE (imputed).

subset

Specifies subset index of clones to be tested.

strt

Aptional strata variable for splitting the data in different strata.

...

Optional parameters passed further along to each of the univariate testing functions.

Value

A data frame similar to the result returned from mt.maxT function from multtest package with components:

index

Vector of row indices, between 1 and nrow(X), where rows are sorted first according to their adjusted $p$-values, next their unadjusted $p$-values, and finally their test statistics.

teststat

Vector of test statistics, ordered according to index. To get the test statistics in the original data order, use teststat[order(index)].

rawp

Vector of raw (unadjusted) $p$-values, ordered according to index.

adjp

Vector of adjusted $p$-values, ordered according to index.

See Also

aCGH, Surv, mt.maxT, coxph, survdiff, p.adjust