estimatePatterns: Estimate distribution of methylation patterns

In MPFE: Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data

Description

Estimate distribution of methylation patterns from a table of counts from a bisulphite sequencing experiment given a non-conversion rate and a sequencing error rate.

Usage

  estimatePatterns(patternCounts,
                   epsilon=0,
                   eta=0,
                   column=NULL,
                   fast=TRUE,
                   steps=20000,
                   reltol=1e-12)

Arguments

patternCounts	data frame with methylation patterns in first column and pattern counts in subsequent columns.
epsilon	non-converson rate, a value between 0 and 1.
eta	error rate, either a vector of numbers between 0 and 1 of length equal to the number of CpG sites or a single value between 0 and 1 for a single error rate across all sites.
column	a vector that specifies the indices of the columns of ‘patternCounts’ to process. Its entries are integer values from 1 to the number of pattern counts columns in ‘patternCounts’. If NULL, defaults to all columns.
fast	logical, if TRUE, fast version implemented (default).
steps	number of steps for the optimiser, passed to constrOptim. If NULL, defaults to 20000 steps.
reltol	relative tolerance for the optimiser, passed to constrOptim. If NULL, defaults to 1e-12.

Value

The function returns a list of data frames.

The data frames contain the following columns:

pattern	the list of input patterns (factor)
coverage	the number of reads for each pattern (integer)
observedDistribution	the observed frequencies of each pattern (numeric)
estimatedDistribution	the estimated frequencies (numeric)
spurious	indicates whether the patterns are real or spurious (logical)

Author(s)

Peijie Lin, Sylvain Foret, Conrad Burden

Examples

  data(patternsExample)
  estimatePatterns(patternsExample, 
                   epsilon=0.02, 
                   eta=0.01)
  estimatePatterns(patternsExample, 
                   epsilon=0.01, 
                   eta=c(0.015, 0.01, 0.01, 0.01, 0.015),
                   column=2)

MPFE documentation built on Nov. 8, 2020, 7:49 p.m.