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

Description Usage Arguments Value

View source: R/analysis.r

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

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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 17, 2017, 3:59 p.m.