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
Separate a track by strands (for QC purposes)
Functions for analyzing and plotting average methylation
Cluster average methylation of multiple tracks
Filter intervals set by distance from another intervals set
Filter intervals by number of CpGs
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
Functions for retrieving and operating on tidy_cpgs and patterns
Apply a function on tidy cpgs (internally separated by coordinates)
Extract pattern data from tracks without specifying coordinates
transforms patterns to summary statistics: n,n0,n1,nx,nc,meth and epipoly
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
Functions for analyzing and plotting epipolymorphism
Returns TRUE if pattern is a 'border' pattern
Calculate epipolymorphism of samples
Returns TRUE if pattern is fully methylated / unmethylated and FALSE if not
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
Set global definitions
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
check if tidy_cpgs exist for track
Wrapper around gtrack.import_mappedseq for (multiple) bam files
Creates a virtual track and runs gextract
Smoothscatter that works with the pipe operator