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.

AuthorKatherine S. Pollard, Houston N. Gilbert, Yongchao Ge, Sandra Taylor, Sandrine Dudoit
Date of publicationNone
MaintainerKatherine S. Pollard <katherine.pollard@gladstone.ucsf.edu>
LicenseLGPL
Version2.30.0

View on Bioconductor

Functions

ABH.h0 Man page
as.list Man page
as.list,EBMTP-method Man page
as.list-methods Man page
as.list,MTP-method Man page
blockFX Man page
boot.null Man page
boot.resample Man page
center.only Man page
center.scale Man page
corr.null Man page
corr.Tn Man page
coxY Man page
dens.est Man page
diffmeanX Man page
diffs.1.N Man page
EBMTP Man page
ebmtp2mtp Man page
ebmtp2mtp,EBMTP-method Man page
ebmtp2mtp-methods Man page
EBMTP-class Man page
[,EBMTP-method Man page
EBMTP-method Man page
EBMTP-methods Man page
EBupdate Man page
EBupdate,EBMTP-method Man page
EBupdate-methods Man page
fwer2fdr Man page
fwer2gfwer Man page
fwer2tppfp Man page
FX Man page
get.index Man page
get.Tn Man page
golub Man page
golub.cl Man page
golub.gnames Man page
G.VS Man page
Hsets Man page
IC.Cor.NA Man page
IC.CorXW.NA Man page
insert.NA Man page
lmX Man page
lmY Man page
marg.samp Man page
meanX Man page
[-methods Man page
.mt.BLIM Man page
mt.checkclasslabel Man page
mt.checkothers Man page
mt.checkV Man page
mt.checkX Man page
mt.getmaxB Man page
mt.legend Man page
mt.maxT Man page
mt.minP Man page
mt.na2number Man page
.mt.naNUM Man page
mt.niceres Man page
mt.number2na Man page
MTP Man page
mtp2ebmtp Man page
mtp2ebmtp-methods Man page
mtp2ebmtp,MTP-method Man page
MTP-class Man page
mt.plot Man page
[,MTP-method Man page
MTP-methods Man page
.mt.RandSeed Man page
mt.rawp2adjp Man page
mt.reject Man page
mt.sample.label Man page
mt.sample.rawp Man page
mt.sample.teststat Man page
mt.teststat Man page
mt.teststat.num.denum Man page
mt.transformL Man page
mt.transformV Man page
mt.transformX Man page
plot Man page
plot,EBMTP,ANY-method Man page
plot-methods Man page
plot,MTP,ANY-method Man page
print,EBMTP-method Man page
print-methods Man page
print.MTP Man page
print,MTP-method Man page
quant.trans Man page
sd.maxT Man page
sd.minP Man page
ss.maxT Man page
ss.minP Man page
summary Man page
summary,EBMTP-method Man page
summary-methods Man page
summary,MTP-method Man page
tQuantTrans Man page
twowayFX Man page
update Man page
update-methods Man page
update,MTP-method Man page
VScount Man page
wapply Man page

Files

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

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