maPerm: Permute or Bootstrap DMR Detection

In jeffbhasin/methylaction: MethylAction: Differentially Methylated Regions (DMRs) from MBD-isolated Genome Sequencing (MiGS/MBD-seq)

Description

Will perform permutations or bootstraps after methylaction() has been called. See also maPermMerge() and maPermFdr().

Usage

maPerm(ma, reads, nperms, combos = NULL, save = T, perm.boot = F,
  ncore = 1)

Arguments

ma	Output object from methylaction()
reads	Preprocessed reads/fragments data from getReads()
nperms	Number of permutation (or bootstrap) iterations to perform
combos	A matrix of pre-set combinations to use. Useful for smaller sample sizes where there are only a limited number of possible combinations. The row should have ncols = number of samples, and each row represents a re-ordering of samples into groups (where the groups will be set in the order they appear in the "samp" given to methylaction())
save	If true, save an RData file of the permutations. These can be merged using maPermMerge(). Useful for running permutations across multiple computers or in a cluster environment. If FALSE, will return the permutation results.
perm.boot	If nperms > 0 and if TRUE, perform bootstrapping (sampling with replacement). Otherwise, perform permutations (sampling without permutations)
ncore	Number of parallel processes to use

Value

A list of DMRs arising from each permutation or bootstrap. Will save as an RData if save==TRUE.

jeffbhasin/methylaction documentation built on May 19, 2019, 1:46 a.m.