runbumphunter: Run bumphunter to obtain DMRs (parameters stolen straight...

Description Usage Arguments Value Examples

View source: R/runbumphunter.R

Description

Run bumphunter to obtain DMRs (parameters stolen straight from bumphunter)

Usage

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runbumphunter(methyl.mat, treatment, covariates, pickCutoff = TRUE,
  pickCutoffQ = 0.975, maxGap = 300, smooth = FALSE, B = 250,
  nullMethod = "bootstrap", n.core = 20)

Arguments

methyl.mat

matrix of samples by methylation DMS

covariates

matrix (samples in rows, covar in column) covariates

pickCutoff

Should bumphunter attempt to pick a cutoff using the permutation distribution?

pickCutoffQ

The quantile used for picking the cutoff using the permutation distribution.

maxGap

If cluster is not provided this maximum location gap will be used to define cluster via the clusterMaker function.

smooth

A logical value. If TRUE the estimated profile will be smoothed with the smoother defined by smoothFunction

B

An integer denoting the number of resamples to use when computing null distributions. This defaults to 0. If permutations is supplied that defines the number of permutations/bootstraps and B is ignored. B

nullMethod

Method used to generate null candidate regions, must be one of <e2><80><98>bootstrap<e2><80><99> or <e2><80><98>permutation<e2><80><99> (defaults to <e2><80><98>permutation<e2><80><99>). However, if covariates in addition to the outcome of interest are included in the design matrix (ncol(design)>2), the <e2><80><98>permutation<e2><80><99> approach is not recommended.

n.core

number of cores to run in paralell

Value

annotated data frame; see bumphunter documentation for further explanation of output

Examples

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DMS_annotated=annotateGenes(DMS)

ShanEllis/methylarking documentation built on May 10, 2017, 1:33 p.m.