center.only, center.scale, and quant.trans. Details are given below. These functions are called by MTP and EBMTP.
boot.null(X, label, stat.closure, W = NULL, B = 1000, test, nulldist, theta0 = 0, tau0 = 1, marg.null = NULL, marg.par = NULL, ncp = 0, perm.mat, alternative = "two.sided", seed = NULL, cluster = 1, dispatch = 0.05, keep.nulldist, keep.rawdist)
boot.resample(X, label, p, n, stat.closure, W, B, test)
center.only(muboot, theta0, alternative)
center.scale(muboot, theta0, tau0, alternative)
quant.trans(muboot, marg.null, marg.par, ncp, alternative, perm.mat)exprs(X) is the data of interest and pData(X) may contain outcomes and covariates of interest. For boot.resample X must be a matrix. For currently implemented tests, one hypothesis is tested for each row of the data.MTP function. The closure consists of a function for computing the test statistic and its enclosing environment, with bindings for relevant additional arguments (such as null values, outcomes, and covariates).W must be the same dimension as X with one weight for each value in X. If a vector, W may contain one weight for each observation (i.e. column) of X or one weight for each variable (i.e. row) of X. In either case, the weights are duplicated appropriately. Weighted F-tests are not available. Default is 'NULL'.nulldist is 'perm'). Can be reduced to increase the speed of computation, at a cost to precision. Default is 1000.MTP for a list of tests.center.only is chosen for transforming the raw bootstrap test statistics.nulldist='boot.qt', the marginal null distribution to use for quantile transformation. Can be one of 'normal', 't', 'f' or 'perm'. Default is 'NULL', in which case the marginal null distribution is selected based on choice of test statistics. Defaults explained below. If 'perm', the user must supply a vector or matrix of test statistics corresponding to another marginal null distribution, perhaps one created externally by the user, and possibly referring to empirically derived marginal permutation distributions, although the statistics could represent any suitable choice of marginal null distribution.nulldist='boot.qt', the parameters defining the marginal null distribution in marg.null to be used for quantile transformation. Default is 'NULL', in which case the values are selected based on choice of test statistics and other available parameters (e.g., sample size, number of groups, etc.). Defaults explained below. User can override defaults, in which case a matrix of marginal null distribution parameters can be accepted. Providing a matrix of values allows the user to perform multiple testing using parameters which may vary with each hypothesis, as may be desired in common-quantile minP procedures. In this way, factors affecting multiple testing procedure performance such as sample size or missingness may be assessed.nulldist='boot.qt', a value for a possible noncentrality parameter to be used during marginal quantile transformation. Default is 'NULL'.nulldist='boot.qt' and marg.null='perm', a matrix of user-supplied test statistics from a particular distribution to be used during marginal quantile transformation. The statistics may represent empirically derived marginal permutation values, may be theoretical values, or may represent a sample from some other suitable choice of marginal null distribution.set.seed to set the seed for the random number generator for bootstrap resampling. This argument can be used to repeat exactly a test performed with a given seed. If the seed is specified via this argument, the same seed will be returned in the seed slot of the MTP object created. Else a random seed(s) will be generated, used and returned. Vector of integers used to specify seeds for each node in a cluster used to to generate a bootstrap null distribution.multtest v. 2.0.0 given expanded null distribution options. Previously, this argument was an indicator of whether the bootstrap estimated test statistics distribution should be centered and scaled (to produce a null distribution) or not. If csnull=FALSE, the (raw) non-null bootstrap estimated test statistics distribution was returned. If the non-null bootstrap distribution should be returned, this object is now stored in the 'rawdist' slot when keep.rawdist=TRUE.B*dispatch must be an integer. If dispatch is an integer, then B/dispatch must be an integer. Default is 5 percent.nulldist='perm'. Note that this matrix can be quite large.nulldist='perm' or 'ic'. Note that this matrix can become quite large. If one wishes to use subsequent calls to update in which one updates choice of bootstrap null distribution, keep.rawdist must be TRUE. To save on memory, update only requires that one of keep.nulldist or keep.rawdist be 'TRUE'.keep.rawdist=TRUE, the matrix of non-null, non-transformed bootstrap test statistics. If 'FALSE', an empty matrix with dimension 0-by-0.keep.rawdist=TRUE (default), the matrix of appropriately transformed null test statistics as given by one of center.scale, center.only, or quant.trans. This is the estimated joint test statistics null distribution.Both list elements rawboot and muboot contain matrices of dimension the number of hypotheses (typically nrow(X)) by the number of bootstrap iterations (B). Each row of muboot is the bootstrap estimated marginal null distribution for a single hypothesis. For boot.null and center.scale, each column of muboot is a centered and scaled resampled vector of test statistics. For boot.null and center.only, each column of muboot is a centered, resampled vector of test statistics.For boot.null and quant.trans, each column of muboot is a marginal null quantile-transformed resampled vector of test statistics. For each choice of marginal null distribution (defined by marg.null and marg.par), a random sample of size B is drawn and then rearranged based on the ranks of the marginal test statistics bootstrap distribution corresponding to each hypothesis (typically within rows of X). This means that using quant.trans will set the RNG seed ahead by B * the number of hypotheses (similarly, typically nrow(X)). Tie breaks in the marginal non-null bootstrap distribution are implemented inside the internal function marg.samp called by quant.trans. Default values of marg.null and marg.par are available based on choice of test statistics, sample size 'n', and various other parameters. By the time boot.null is called in either the MTP or EBMTP functions, the default marginal null distribution settings have already been formatted and passed in their correct form to boot.null. These default values correspond to:marg.null and marg.par.The rawboot and muboot objects are returned in the slots rawdist and nulldist of an object of class MTP or EBMTP when the arguments keep.rawdist or keep.nulldist to the MTP function are TRUE. For boot.resample a matrix of bootstrap samples prior to null transformation is returned.
M.J. van der Laan, S. Dudoit, K.S. Pollard (2004), Multiple Testing. Part II. Step-Down Procedures for Control of the Family-Wise Error Rate, Statistical Applications in Genetics and Molecular Biology, 3(1). http://www.bepress.com/sagmb/vol3/iss1/art14/
S. Dudoit, M.J. van der Laan, K.S. Pollard (2004), Multiple Testing. Part I. Single-Step Procedures for Control of General Type I Error Rates, Statistical Applications in Genetics and Molecular Biology, 3(1). http://www.bepress.com/sagmb/vol3/iss1/art13/
Katherine S. Pollard and Mark J. van der Laan, "Resampling-based Multiple Testing: Asymptotic Control of Type I Error and Applications to Gene Expression Data" (June 24, 2003). U.C. Berkeley Division of Biostatistics Working Paper Series. Working Paper 121. http://www.bepress.com/ucbbiostat/paper121
M.J. van der Laan and A.E. Hubbard (2006), Quantile-function Based Null Distributions in Resampling Based Multiple Testing, Statistical Applications in Genetics and Molecular Biology, 5(1). http://www.bepress.com/sagmb/vol5/iss1/art14/
S. Dudoit and M.J. van der Laan. Multiple Testing Procedures and Applications to Genomics. Springer Series in Statistics. Springer, New York, 2008.
corr.null, MTP, MTP-class, EBMTP, EBMTP-class, get.Tn, ss.maxT, mt.sample.teststat,get.Tn, wapply, boot.resample
set.seed(99)
data<-matrix(rnorm(90),nr=9)
#closure
ttest<-meanX(psi0=0,na.rm=TRUE,standardize=TRUE,alternative="two.sided",robust=FALSE)
#test statistics
obs<-get.Tn(X=data,stat.closure=ttest,W=NULL)
#bootstrap null distribution (B=100 for speed, default nulldist, "boot.cs")
nulldistn<-boot.null(X=data,W=NULL,stat.closure=ttest,B=100,test="t.onesamp",
nulldist="boot.cs",theta0=0,tau0=1,alternative="two.sided",
keep.nulldist=TRUE,keep.rawdist=FALSE)$muboot
#bootstrap null distribution with marginal quantile transformation showing
#default values that are passed to marg.null and marg.par arguments
nulldistn.qt<-boot.null(X=data,W=NULL,stat.closure=ttest,B=100,test="t.onesamp",
nulldist="boot.qt",theta0=0,tau0=1,alternative="two.sided",
keep.nulldist=TRUE,keep.rawdist=FALSE,marg.null="t",
marg.par=matrix(9,nr=10,nc=1))$muboot
#unadjusted p-values
rawp<-apply((obs[1,]/obs[2,])<=nulldistn,1,mean)
sum(rawp<=0.01)
rawp.qt<-apply((obs[1,]/obs[2,])<=nulldistn.qt,1,mean)
sum(rawp.qt<=0.01)
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