PsiHat: Several Local False Discovery Rate Estimators
Version 1.0

Suite of R functions for the estimation of local false discovery rate (LFDR) using several methods.

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AuthorAlaa Ali, Kyle Leckett, Marta Padilla, David R. Bickel (contributions from Bradley Efron, Brit B. Turnbull, Balasubramanian Narasimhan from package locfdr).
Date of publication2015-10-05 12:58:12
MaintainerMarta Padilla <padilla.mpf@gmail.com>
LicenseGPL-3
Version1.0
URL http://www.r-project.org http://www.bioconductor.org http://www.statomics.com
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PsiHat")

Man pages

lfdr.bbe: Binomial-based LFDR estimator.
lfdr.elfdr: Expected LFDR (ELFDR).
lfdr.empiricalNull: Histogram-based estimator (HBE).
p0est: Estimates the proportion of unaffected features (p0).
PsiHat-internal: Internal Functions and Methods
PsiHat-package: Several Local False Discovery Rate Estimators
rvalue: Rvalues and qvalues.

Functions

BFDR Man page Source code
CDF-class Man page
Combine Man page
Combine,Numeric,Numeric-method Man page
Combine,Vector,Vector-method Man page
Combine,ttest,ttest-method Man page
Combine-methods Man page
CombinedNames Man page Source code
CorrectLimits Man page
CorrectLimits,numeric-method Man page
CorrectLimits-methods Man page
MakeNames Man page Source code
Matrix-class Man page
Mean Man page
Mean,matrix-method Man page
Mean,numeric-method Man page
Mean-methods Man page
Median Man page
Median,matrix-method Man page
Median,numeric-method Man page
Median-methods Man page
Mfrow Man page Source code
Numeric-class Man page
PHATs.pvalue Man page Source code
PHATs.stat Man page Source code
PValue Man page Source code
PValueFUN Man page Source code
Pbinom Man page Source code
PsiHat Man page
PsiHat-package Man page
Rank Man page
Rank,numeric-method Man page
Rank-methods Man page
Rep Man page
Rep,Vector-method Man page
Rep,matrix-method Man page
Rep,nxprnSet-method Man page
Rep-methods Man page
RepNames Man page Source code
SFDR Man page Source code
Scalar-class Man page
Sd Man page
Sd,numeric-method Man page
Sd-methods Man page
Seq Man page Source code
Slot Man page Source code
Var Man page Source code
Vector-class Man page
[,Matrix,ANY,ANY-method Man page
[,Matrix,ANY,missing-method Man page
[,Matrix,missing,ANY-method Man page
[,Numeric,ANY,missing-method Man page
[,bias.corrected.pvalue,ANY,missing-method Man page
[,cvalue,ANY,missing-method Man page
[,est.lfdr.x,ANY,missing-method Man page
[,nExpressionSet,ANY,ANY-method Man page
[,nExpressionSet,ANY,missing-method Man page
[,nExpressionSet,missing,ANY-method Man page
[,nxprnSet,ANY,ANY-method Man page
[,nxprnSet,ANY,missing-method Man page
[,nxprnSet,missing,ANY-method Man page
[,nxprnSetPair,ANY,missing-method Man page
[,ttest,ANY,missing-method Man page
[-methods Man page
[<-,Matrix,ANY,missing-method Man page
[<-,Numeric,ANY,missing-method Man page
[<--methods Man page
alt-class Man page
are Man page Source code
are_null Man page Source code
are_prob Man page Source code
are_unk Man page Source code
as.numeric,est.lfdr.x-method Man page
as.numeric-methods Man page
as_colmatrix Man page Source code
as_rowmatrix Man page Source code
assert.are Man page Source code
assert.is Man page Source code
assumedNull Man page Source code
b.notrobust Man page Source code
b.robust Man page Source code
bias.corrected.pvalue-class Man page
binom_BFDR Man page Source code
binom_limit Man page Source code
binom_prob Man page Source code
binom_rBFDR Man page Source code
binom_rprob Man page Source code
blank.plot Man page Source code
blank_CDF Man page Source code
coerce,Numeric,numeric-method Man page
coerce,bias.corrected.pvalue,numeric-method Man page
coerce,cvalue,numeric-method Man page
coerce,nExpressionSet,nXprnSet-method Man page
coerce,nExpressionSet,numeric-method Man page
coerce,nExpressionSet,nxprnSet-method Man page
coerce,nxprnSet,nExpressionSet-method Man page
coerce,nxprnSet,numeric-method Man page
coerce,nxprnSetPair,nxprnSet-method Man page
coerce,ttest,cvalue-method Man page
coerce-methods Man page
coerce<-,Numeric,numeric-method Man page
coerce<-,bias.corrected.pvalue,numeric-method Man page
coerce<--methods Man page
coercenExpressionSet Man page Source code
colnames,ANY-method Man page
colnames,nd1class-method Man page
colnames-methods Man page
colnames<-,ANY,ANY-method Man page
colnames<-,nd1class,nd1class-method Man page
colnames<--methods Man page
compatible Man page Source code
confidence_CDF Man page Source code
cvalue-class Man page
default Man page Source code
dim,nxprnSet-method Man page
dim,nxprnSetPair-method Man page
dim-methods Man page
dimnames,nxprnSet-method Man page
dimnames,nxprnSetPair-method Man page
dimnames-methods Man page
empiricalNull-class Man page
est.lfdr.pvalue-class Man page
est.lfdr.stat-class Man page
est.lfdr.x-class Man page
est2list Man page Source code
estimated.BFDR Man page Source code
estimated.LFDR Man page Source code
exp,nExpressionSet-method Man page
exp,nxprnSet-method Man page
exp,nxprnSetPair-method Man page
exp-methods Man page
expected.lfdr Man page Source code
geomean Source code
get_other.from.testfun Man page Source code
get_pvalues Man page Source code
get_stats Man page Source code
grep_or Man page Source code
grepl_or Man page Source code
harmmean Source code
hsm Man page Source code
indSortAsY Man page Source code
internals Man page
isInteger Man page Source code
is_any Man page
is_err Man page Source code
is_error Man page Source code
is_nd1class Man page Source code
is_nd2class Man page Source code
is_paired Man page
is_paired,nd1class,nd1class-method Man page
is_paired,nd1class,nd2class-method Man page
is_paired,nd2class,nd1class-method Man page
is_paired,nd2class,nd2class-method Man page
is_paired-methods Man page
is_positive Man page
is_positive,nd1class-method Man page
is_positive,nd2class-method Man page
is_positive-methods Man page
is_prob Man page
is_prob,est.lfdr.pvalue-method Man page
is_prob,est.lfdr.stat-method Man page
is_prob,numeric-method Man page
is_prob-methods Man page
is_unique Man page Source code
is_unk Man page Source code
is_vide Man page
k.add.NA.col.dataframe Source code
k.bbe Source code
k.bindSort Source code
k.cbind Source code
k.checkings.hbe Source code
k.checkings.pvalue Source code
k.elfdr Source code
k.empNull Source code
k.get.from.funtest Source code
k.get.from.funtest.mat Source code
k.hbe.method Source code
k.indSort Source code
k.locfdr2est.lfdr.pvalue Source code
k.new_est.lfdr.x Source code
k.qvalue Source code
k.rvalue Source code
k.valid.x Source code
length,cvalue-method Man page
length,est.lfdr.x-method Man page
length,nExpressionSet-method Man page
length,nxprnSet-method Man page
length,nxprnSetPair-method Man page
length,ttest-method Man page
length-methods Man page
lfdr Man page Source code
lfdr.assumedNull Man page Source code
lfdr.bbe Man page Source code
lfdr.bbe1 Man page Source code
lfdr.elfdr Man page Source code
lfdr.empiricalNull Man page Source code
lfdr.hbe Man page Source code
lfdr.hbea Man page Source code
lfdr.hbee Man page Source code
list2est Man page Source code
list2matrix Man page Source code
loccov Man page Source code
loccov2 Man page Source code
locfdr Man page Source code
locfdr.rname Man page Source code
locmle Man page Source code
log_lfdr_se Man page Source code
logb,ANY,ANY-method Man page
logb,nExpressionSet,missing-method Man page
logb,nXprnSet,missing-method Man page
logb,nxprnSet,missing-method Man page
logb,nxprnSetPair,missing-method Man page
logb-methods Man page
make_labels Man page Source code
matrix2list Man page Source code
monotonic.pvalue Man page Source code
nCDF Man page Source code
nExpressionSet-class Man page
nMatrix Man page
nMatrix,matrix-method Man page
nMatrix,numeric-method Man page
nMatrix-methods Man page
nNumeric Man page
nNumeric,numeric-method Man page
nNumeric-methods Man page
nScalar Man page
nScalar,ANY-method Man page
nScalar-methods Man page
nXprnSet-class Man page
nalt Man page Source code
names,cvalue-method Man page
names,est.lfdr.x-method Man page
names,nExpressionSet-method Man page
names,nxprnSet-method Man page
names,nxprnSetPair-method Man page
names,ttest-method Man page
names-methods Man page
names<-,est.lfdr.x,character-method Man page
names<--methods Man page
nannotation Man page
nannotation,nExpressionSet-method Man page
nannotation,nxprnSet-method Man page
nannotation,nxprnSetPair-method Man page
nannotation-methods Man page
ncbind Man page Source code
ncol,ANY-method Man page
ncol,NULL-method Man page
ncol,nd1class-method Man page
ncol-methods Man page
ncvalue Man page Source code
nd1class-class Man page
nd2class-class Man page
nempiricalNull Man page Source code
new_CDF Man page Source code
new_alt Man page Source code
new_bias.corrected.pvalue Man page Source code
new_cvalue Man page Source code
new_empiricalNull Man page Source code
new_est.lfdr.pvalue Man page Source code
new_est.lfdr.stat Man page Source code
new_nExpressionSet Man page Source code
new_nXprnSet Man page Source code
new_nxprnSet Man page Source code
new_nxprnSetPair Man page
new_nxprnSetPair,matrix,matrix,missing-method Man page
new_nxprnSetPair,nXprnSet,nXprnSet,missing-method Man page
new_nxprnSetPair,nxprnSet,missing,character-method Man page
new_nxprnSetPair,nxprnSet,nxprnSet,missing-method Man page
new_nxprnSetPair-methods Man page
new_ttest Man page Source code Source code
nexprs Man page
nexprs,nExpressionSet-method Man page
nexprs,nXprnSet-method Man page
nexprs,nxprnSet-method Man page
nexprs,nxprnSetPair-method Man page
nexprs-methods Man page
nexprs<- Man page
nexprs<-,nExpressionSet,matrix-method Man page
nexprs<-,nExpressionSet,numeric-method Man page
nexprs<-,nxprnSet,matrix-method Man page
nexprs<-,nxprnSet,numeric-method Man page
nexprs<--methods Man page
nfData Man page
nfData,nExpressionSet-method Man page
nfData,nxprnSet-method Man page
nfData,nxprnSetPair-method Man page
nfData-methods Man page
nfeatureNames Man page
nfeatureNames,nExpressionSet-method Man page
nfeatureNames,nxprnSet-method Man page
nfeatureNames,nxprnSetObjectPair-method Man page
nfeatureNames,nxprnSetPair-method Man page
nfeatureNames-methods Man page
npData Man page
npData,nExpressionSet-method Man page
npData,nxprnSet-method Man page
npData,nxprnSetPair-method Man page
npData-methods Man page
nprnSet2matrix Man page Source code
nqvalue Man page Source code
nrbind Man page Source code
nrow,ANY-method Man page
nrow,NULL-method Man page
nrow,nd1class-method Man page
nrow-methods Man page
nscalar Man page
nscalar,ANY-method Man page
nscalar,numeric-method Man page
nscalar,scalar-method Man page
nscalar-methods Man page
nsize Man page Source code
nttest Man page Source code
nunique Man page
nx11 Man page Source code
nxprnSet-class Man page
nxprnSetObject-class Man page
nxprnSetObjectPair-class Man page
nxprnSetObjects-class Man page
nxprnSetPair-class Man page
nxprnSubset Man page
nxprnSubset,nExpressionSet-method Man page
nxprnSubset,nxprnSet-method Man page
nxprnSubset-methods Man page
p0est Man page Source code
prep.2matrices Man page Source code
print,ANY-method Man page
print,nExpressionSet-method Man page
print,nXprnSet-method Man page
print,nxprnSet-method Man page
print,nxprnSetPair-method Man page
print-methods Man page
printGeneric Man page Source code
printInvalid Man page Source code
print_stats Man page Source code
probability_CDF Man page Source code
pval2stat Man page Source code
removeEQ.from.matrix Man page Source code
removeMissing Man page
removeMissing,nxprnSet-method Man page
removeMissing,nxprnSetPair-method Man page
removeMissing-methods Man page
removeNA.from.matrix Man page Source code
removeRC.from.matrix Man page Source code
rownames,ANY-method Man page
rownames,nd1class-method Man page
rownames-methods Man page
rvalue Man page Source code
s3 Man page
s3,ANY,character-method Man page
s3,ANY,missing-method Man page
s3-methods Man page
s3_recursive Man page Source code
sameAsX_names Man page Source code
sameAsY Man page Source code
sameLengths Man page Source code
sameNames Man page
sameNames,ANY-method Man page
sameNames-methods Man page
sameXY_names Man page Source code
sample_size Man page
sample_size,matrix-method Man page
sample_size,numeric-method Man page
sample_size,nxprnSet-method Man page
sample_size-methods Man page
scalar-class Man page
se.mean Man page Source code
silence Man page Source code
sorted Man page Source code Source code
spline.des Man page
stat2pval Man page Source code
stats Man page Source code
string2char Man page Source code
string2vect Source code
t_test_CDF Man page Source code
ttest-class Man page
undefAsNA Man page Source code
vect2string Man page Source code
wilkinson.test Man page Source code

Files

NAMESPACE
R
R/00001Dutils.R
R/000092PSIhat.v0.R
R/00000Mutils.R
R/000091HBE.R
R/00005DeLocfdr.R
R/00006Vario.R
R/00002DMutils.R
R/00001Mutils.R
R/00000Dutils.R
MD5
DESCRIPTION
man
man/rvalue.Rd
man/PsiHat-package.Rd
man/PsiHat-internal.Rd
man/lfdr.elfdr.Rd
man/lfdr.bbe.Rd
man/p0est.Rd
man/lfdr.empiricalNull.Rd
PsiHat documentation built on May 20, 2017, 4:47 a.m.