# Tools for computational epigenomics

## Documentation for package ‘compEpiTools’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

compEpiTools-package | Tools for computational epigenomics
compEpiTools | Tools for computational epigenomics
countOverlapsInBins | given a query and a subject GRanges returns a matrix of counts of subject in bins of query
countOverlapsInBins-method | given a query and a subject GRanges returns a matrix of counts of subject in bins of query
countOverlapsInBins-methods | given a query and a subject GRanges returns a matrix of counts of subject in bins of query
distanceFromTSS | Returns the GRanges annotated with info about the closer TSS
distanceFromTSS-method | Returns the GRanges annotated with info about the closer TSS
distanceFromTSS-methods | Returns the GRanges annotated with info about the closer TSS
enhancers | A GRanges method to define enhancers based on H3K4me1 peaks
enhancers-method | A GRanges method to define enhancers based on H3K4me1 peaks
enhancers-methods | A GRanges method to define enhancers based on H3K4me1 peaks
featuresLength | Utilities to transform a TxDb into a GTF file
featuresLength-method | Utilities to transform a TxDb into a GTF file
featuresLength-methods | Utilities to transform a TxDb into a GTF file
findLncRNA | Identify putative long non coding RNAs (lncRNA)
getPromoterClass | Determining the CpG promoter class and the average CpG content
getPromoterClass-method | Determining the CpG promoter class and the average CpG content
getPromoterClass-methods | Determining the CpG promoter class and the average CpG content
GR2fasta | A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome
GR2fasta-method | A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome
GR2fasta-methods | A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome
GRanges2ucsc | A GRanges method to convert ranges information into UCSC format
GRanges2ucsc-method | A GRanges method to convert ranges information into UCSC format
GRanges2ucsc-methods | A GRanges method to convert ranges information into UCSC format
GRangesInPromoters | Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters
GRangesInPromoters-method | Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters
GRangesInPromoters-methods | Based on a GRanges and a TxDb, subsets the GRanges to those regions overalpping with promoters
GRannotate | Based on a GRanges and a TxDb, returns the GRanges with a series of annotations
GRannotate-method | Based on a GRanges and a TxDb, returns the GRanges with a series of annotations
GRannotate-methods | Based on a GRanges and a TxDb, returns the GRanges with a series of annotations
GRannotateSimple | a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic
GRannotateSimple-method | a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic
GRannotateSimple-methods | a GRanges method to split a GRanges in three GRanges: promoter, intragenic and intergenic
GRbaseCoverage | Based on a GRanges and a BAM file, returns a list of base coverage vectors for each range
GRbaseCoverage-method | Based on a GRanges and a BAM file, returns a list of base coverage vectors for each range
GRbaseCoverage-methods | Based on a GRanges and a BAM file, returns a list of base coverage vectors for each range
GRcoverage | based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverage-method | based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverage-methods | based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverageInbins | based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverageInbins-method | based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverageInbins-methods | based on a GRanges and a BAM file, returns the total coverage for each range, or for each bin of the range.
GRcoverageSummit | Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range
GRcoverageSummit-method | Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range
GRcoverageSummit-methods | Based on a GRanges and a BAM file, returns a GRanges with the positions of maximum coverage within each range
GRenrichment | Determines the enrichment over a set of genomic regions given two BAM files
GRenrichment-method | Determines the enrichment over a set of genomic regions given two BAM files
GRenrichment-methods | Determines the enrichment over a set of genomic regions given two BAM files
GRmidpoint | Returns a GRanges containing the mid point of a GRanges
GRmidpoint-method | Returns a GRanges containing the mid point of a GRanges
GRmidpoint-methods | Returns a GRanges containing the mid point of a GRanges
GRsetwidth | Set the width of a GRanges based on the mid point of each region
GRsetwidth-method | Set the width of a GRanges based on the mid point of each region
GRsetwidth-methods | Set the width of a GRanges based on the mid point of each region
heatmapData | Based on a list of GRanges, determine various kind of counts before displaying a heatmap
heatmapPlot | displays the heatmap based on the data from heatmapData
makeGtfFromDb | Utilities to transform a TxDb into a GTF file
makeGtfFromDb-method | Utilities to transform a TxDb into a GTF file
makeGtfFromDb-methods | Utilities to transform a TxDb into a GTF file
matchEnhancers | GRanges method to match enhancers with putative targets sites
matchEnhancers-method | GRanges method to match enhancers with putative targets sites
matchEnhancers-methods | GRanges method to match enhancers with putative targets sites
overlapOfGRanges | visualization of GRanges overlap
overlapOfGRanges-method | visualization of GRanges overlap
overlapOfGRanges-methods | visualization of GRanges overlap
palette2d | build a two dimensional color palette
plotStallingIndex | Stalling Index plots
simplifyGOterms | simplify a list of GO terms
stallingIndex | returns a list with average read count on TSS, gene body, and stalling index for a number of samples
topGOres | determines GeneOntology (GO) enriched terms for a set of Entrez gene ids
TSS | based on a TxDb returns a GRanges with the TSS positions for all transcripts
ucsc2GRanges | Convert UCSC-formatted genomic positions into a GRanges
unionMaxScore | GRanges method to perform union of peaks keeping the score of the most significant peak
unionMaxScore-method | GRanges method to perform union of peaks keeping the score of the most significant peak
unionMaxScore-methods | GRanges method to perform union of peaks keeping the score of the most significant peak