aCGH.test {aCGH}R Documentation

Testing association of aCGH clones with censored or continuous outcomes


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.


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


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.
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.


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.


Peter Dimitrov

See Also

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


[Package aCGH version 1.1.4 Index]