plot.bum: Quantile-quantile plot for the beta-uniform mixture model

In BioNet: Routines for the functional analysis of biological networks

Description

The function plot the theoretical quantiles of the fitted bum model against the quantiles of the observed p-value distribution.

Usage

## S3 method for class 'bum'
plot(x, main="QQ-Plot", xlab="Estimated p-value", ylab="Observed p-value", ...)

Arguments

x	Maximum likelihood estimation object of the fitted bum model.
main	An overall title for the plot.
xlab	A title for the x axis.
ylab	A title for the y axis.
...	Other graphic parameters for the plot.

Author(s)

Daniela Beisser

See Also

fitBumModel, plot.bum, bumOptim

Examples

data(pvaluesExample)
pvals <- pvaluesExample[,1]
mle <- fitBumModel(pvals, plot=FALSE)
plot(mle)

Example output

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

BioNet documentation built on Nov. 8, 2020, 5:48 p.m.