Description Usage Arguments Value Author(s) References See Also Examples
The function calculates the p-value threshold tau for a given false discovery rate. Tau is used for the scoring function.
1 | fdrThreshold(fdr, fb)
|
fdr |
False discovery rate. |
fb |
Model from the beta-uniform mixture fitting. |
P-value threshold tau.
Marcus Dittrich
S. Pounds, S.W. Morris (2003) Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values. Bioinformatics, 19(10): 1236-1242.
1 2 3 4 5 | data(pvaluesExample)
pvals <- pvaluesExample[,1]
bum.mle <- fitBumModel(pvals, plot=FALSE)
tau <- fdrThreshold(fdr=0.001, fb=bum.mle)
tau
|
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: RBGL
[1] 1.973995e-08
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