multtest: Resampling-based multiple hypothesis testing

Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.

Author
Katherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit
Date of publication
None
Maintainer
Katherine S. Pollard <katherine.pollard@gladstone.ucsf.edu>
License
LGPL
Version
2.30.0

View on Bioconductor

Man pages

boot.null
Non-parametric bootstrap resampling function in package...
corr.null
Function to estimate a test statistics joint null...
EBMTP
A function to perform empirical Bayes resampling-based...
EBMTP-class
Class "EBMTP", classes and methods for empirical Bayes...
fwer2gfwer
Function to compute augmentation MTP adjusted p-values
get.index
Function to compute indices for ordering hypotheses in...
golub
Gene expression dataset from Golub et al. (1999)
Hsets
Functions for generating guessed sets of true null hypotheses...
meanX
Functions to create test statistic closures and apply them to...
mt.internal
Internal multtest functions and variables
mt.maxT
Step-down maxT and minP multiple testing procedures
MTP
A function to perform resampling-based multiple hypothesis...
MTP-class
Class "MTP", classes and methods for multiple testing...
mt.plot
Plotting results from multiple testing procedures
MTP-methods
Methods for MTP and EBMTP objects in Package 'multtest'
mt.rawp2adjp
Adjusted p-values for simple multiple testing procedures
mt.reject
Identity and number of rejected hypotheses
mt.sample.teststat
Permutation distribution of test statistics and raw...
mt.teststat
Computing test statistics for each row of a data frame
ss.maxT
Procedures to perform multiple testing
wapply
Weighted version of the apply function

Files in this package

multtest/DESCRIPTION
multtest/NAMESPACE
multtest/R
multtest/R/EBMTP.R
multtest/R/EBzzz.R
multtest/R/ICQTNullDist.R
multtest/R/mt.basic.R
multtest/R/mt.func.R
multtest/R/nulldistn_c.R
multtest/R/statistics.R
multtest/R/test.R
multtest/R/zzz.R
multtest/data
multtest/data/golub.RData
multtest/inst
multtest/inst/CITATION
multtest/inst/otherDocs
multtest/inst/otherDocs/MTP.Rnw
multtest/inst/otherDocs/MTPALL.Rnw
multtest/inst/otherDocs/multtest.Rnw
multtest/man
multtest/man/EBMTP-class.Rd
multtest/man/EBMTP.Rd
multtest/man/Hsets.Rd
multtest/man/MTP-class.Rd
multtest/man/MTP-methods.Rd
multtest/man/MTP.Rd
multtest/man/boot.null.Rd
multtest/man/corr.null.Rd
multtest/man/fwer2gfwer.Rd
multtest/man/get.index.Rd
multtest/man/golub.Rd
multtest/man/meanX.Rd
multtest/man/mt.internal.Rd
multtest/man/mt.maxT.Rd
multtest/man/mt.plot.Rd
multtest/man/mt.rawp2adjp.Rd
multtest/man/mt.reject.Rd
multtest/man/mt.sample.teststat.Rd
multtest/man/mt.teststat.Rd
multtest/man/ss.maxT.Rd
multtest/man/wapply.Rd
multtest/src
multtest/src/Makevars
multtest/src/Makevars.win
multtest/src/Rpack.c
multtest/src/VScount.c
multtest/src/block_sampling_fixed.c
multtest/src/bootloop.c
multtest/src/mt.c
multtest/src/mt.h
multtest/src/pairt_sampling.c
multtest/src/pairt_sampling_fixed.c
multtest/src/random.c
multtest/src/sampling.c
multtest/src/sampling_fixed.c
multtest/src/stat_func.c
multtest/src/stat_order.c
multtest/vignettes
multtest/vignettes/MTP.pdf
multtest/vignettes/MTP.tex
multtest/vignettes/MTPALL.pdf
multtest/vignettes/golub.R
multtest/vignettes/multtest.bib
multtest/vignettes/multtest.pdf