methylaction: Detect differentially methylated regions (DMRs) from windowed...

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

Description

After the counts have been pre-processed, this function performs all the analysis. Detailed results from intermediate steps are stored in the output list object to analyze method performance and provide input for the summary, export, and plotting functions.

Usage

methylaction(samp, counts, reads, poifdr = 0.1, stageone.p = 0.05,
  anodev.p = 0.05, post.p = 0.05, freq = 2/3, minsize = 150,
  joindist = 200, adjust.var = NULL, nperms = 0, perm.boot = F,
  ncore = 1)

Arguments

samp	Sample data.frame from readSampleInfo()
counts	Preprocessed count data from getCounts()
reads	Preprocessed reads/fragments data from getReads()
poifdr	False discovery rate to use during initial filtering and frequency calling. Changing this value will change the threshold used for calling the presence of methylation.
stageone.p	P-value cutoff for the pairwise testing in stage one.
anodev.p	P-value cutoff for the analysis of deviance (ANODEV) in stage two testing.
post.p	P-value cutoff for post-tests in stage two testing.
freq	Fraction of samples within groups that must agree with respect to methylation status in order for "frequent" to be "TRUE" in the output DMR list.
minsize	Minimum size of DMRs to report (in bp)
joindist	Extend significant windows into DMRs over non-significant stage one windows between them up to this distance large (in bp)
adjust.var	Name of a column present in "samp" that will be used as a covariate adjustment in the stage two ANODEV generalized linear model (GLM)
nperms	Optional, perform this number of permutations after calling DMRs. Will create a data.table called "FDR" in the output list. See also maPerm(), maPermMerge(), and maPermFdr() for manual permutation running and FDR calculation.
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 containing detailed results from each stage of the analysis.

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