PsiHat: Several Local False Discovery Rate Estimators

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

Install the latest version of this package by entering the following in R:
install.packages("PsiHat")
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
http://www.r-project.org
http://www.bioconductor.org, http://www.statomics.com

View on CRAN

Functions

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

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