Learn R Programming

BiSeq (version 1.12.0)

Processing and analyzing bisulfite sequencing data

Description

The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.

Copy Link

Version

Version

1.12.0

License

LGPL-3

Maintainer

Katja Hebestreit

Last Published

February 15th, 2017

Functions in BiSeq (1.12.0)

RRBS data of APL patient samples and controls.

A GRanges of promoters of the human genome

Estimates the correlations of the z-scores

Plots raw and smoothed methylation data for a given region

betaResultsNull

The output of betaRegression for resampled data

Prints a short summary of coverage statistics per sample

The output of predictMeth

Test whether at least one CpG is differentially methylated in a given genomic region

The output of findDMRs

annotateGRanges

Annotates a GRanges object by means of a second GRanges object

Reads cytosine methylation stati determined by Bismark

summarizeRegions

Aggregates methylation information of single CpG sites

The output of betaRegression

Class to contain Bisulfite Sequencing (BiSeq) Data

compareTwoSamples

Detects DMRs by comparing two samples

Predicts methylation levels along CpG sites or for a grid of sites in CpG clusters.

Variogram estimator.

A function to estimate and test a group factor within a beta regression

Writes BSraw and BSrel data to a bed file suitable for the IGV

Aggregates CpG sites to DMRs

Plots methylation values of multiple samples in a given region

clusterSitesToGR

A function to obtain a GRanges object of CpG clusters from BSraw and BSrel objects

filterBySharedRegions

Reduces a BSraw or BSrel object to regions (or single CpGs) shared by a fraction of samples

Converts a BSraw object to a BSrel object

Limits the coverage of a BSraw object

Output of makeVariogram

smoothVariogram

Smoothes variogram

Class to contain raw Bisulfite Sequencing (BiSeq) Data

Filters regions (or single CpGs) of a BSraw object with a minimum coverage

plotBindingSites

Plots the mean methylation of given regions

logisticRegression

Estimates and tests a group factor

Tests CpG clusters

Assigns CpG cluster memberships on CpG sites within BSraw objects

Plots smoothed methylation values for a bunch of samples and a given region

Trims CpG clusters

Creates boxplots of coverages per sample

binomLikelihoodSmooth

Calculates local likelihood estimations for binomial random variables