Importing datasets

Functions for importing datasets to gpatterns

Change tidy_cpgs coordinates to fragments coordinates

Create an bowtie2 index for a bisulfite converted genome

Align bisulfite converted reads to a reference genome using bowtie2

Creates patterns attributes of track

Calculate QC statistics for track

Create a track from bam files.

Create a track from tidy_cpgs files

Merge tracks

Separate a track by strands (for QC purposes)

Average methylation

Functions for analyzing and plotting average methylation

Cluster average methylation of multiple tracks

count CpGs in intervals

Filter intervals set by distance from another intervals set

Filter intervals by number of CpGs

Extract average methylation

Get fragment coverage

Define promoter regions

Plot global methylation stratified on other tracks

Get coverage of intervals in multiple tracks

Plot CpG correlation (pearson) as a function of distance between CpGs

Plot a heatmap of average methylation clustering

screen intervals by coverage in multiple tracks

Plots smoothScatter of average methylation of two tracks

Plot spatial trend of methylation around intervals

Tidy CpGs Functions

Functions for retrieving and operating on tidy_cpgs and patterns

Apply a function on tidy cpgs (internally separated by coordinates)

Downsample patterns table

Extract pattern data from tracks without specifying coordinates

Extract patterns of a track

Extract pattern data

transforms patterns to summary statistics: n,n0,n1,nx,nc,meth and epipoly

Get tidy cpgs from a track

Pattern generation functions

Functions for generating methylation patterns

Calculate pattern coverage for each CpG

Generate pattern space for specific genomic loci

Generate CpG pattern frequency from tidy_cpgs

Generate pileup form tidy_cpgs

Extracts patterns given pattern space

Get pattern space of a track

Generate pattern space

Epipolymorphism functions

Functions for analyzing and plotting epipolymorphism

Returns TRUE if pattern is a 'border' pattern

Run bipolar model

Calculate epipolymorphism of samples

Returns TRUE if pattern is fully methylated / unmethylated and FALSE if not

Plots epipolymorphism

Chip-seq functions

Functions for analyzing chipseq data

Calculate peaks of chip-seq tracks

Plot chip-seq singal with quantile lines

Define putative enhancer regions from chip-seq tracks

Global definitions

Set global definitions

Set parallel threads


Utility functions

Build a gradient pallete based on colors at specific values.

Return an alternate empirical cumulative distribution, counting only

split genomic intervals to bins

Runs R commands on a cluster that supports SGE

Returns the result of track expressions evaluation for each of the

Filter intervals set by distance to another.

Finds neighbors between two sets of intervals (and does not return conflicting column names)

Apply a function on track expression in intervals

Returns a list of track names

check if tidy_cpgs exist for track

Import array from data frame

Wrapper around gtrack.import_mappedseq for (multiple) bam files

Creates a virtual track and runs gextract

Smoothscatter that works with the pipe operator

wrapper around pheatmap

Effiecient implementation of kmeans++ algorithm

Alternative interface for TGL_kmeans