chipenrich: Gene Set Enrichment For ChIP-seq Peak Data
Version 2.0.1

ChIP-Enrich performs gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.

AuthorRyan P. Welch [aut, cph], Chee Lee [aut], Raymond G. Cavalcante [aut, cre], Chris Lee [aut], Laura J. Scott [ths], Maureen A. Sartor [ths]
Bioconductor views ChIPSeq Epigenetics FunctionalGenomics GeneSetEnrichment HistoneModification Regression
Date of publicationNone
MaintainerRaymond G. Cavalcante <rcavalca@umich.edu>
LicenseGPL-3
Version2.0.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("chipenrich")

Getting started

README.md
`chipenrich`: Gene Set Enrichment For ChIP-seq Peak Data

Popular man pages

assign_peak_segments: Assign whole peaks to all overlapping defined gene loci.
chipenrich_package: chipenrich: Gene Set Enrichment For ChIP-seq Peak Data
genome_to_orgdb: Get Entrez ID to gene symbol mappings for custom locus...
load_peaks: Convert a BEDX+Y data.frame and into GRanges
plot_dist_to_tss: Plot histogram of distance from peak to nearest TSS
read_geneset: Function to read custom gene sets from file
read_mappa: Function to read custom mappability files
See all...

All man pages Function index File listing

Man pages

assign_peaks: Assign peak midpoints to defined gene loci.
assign_peak_segments: Assign whole peaks to all overlapping defined gene loci.
broadenrich: Run Broad-Enrich on broad genomic regions
calc_peak_gene_overlap: Add peak overlap and ratio to result of...
chipenrich: Run ChIP-Enrich on narrow genomic regions
chipenrich_package: chipenrich: Gene Set Enrichment For ChIP-seq Peak Data
filter_genesets: Function to filter genesets by locus definition and size
genome_to_organism: Get the correct organism code based on genome
genome_to_orgdb: Get Entrez ID to gene symbol mappings for custom locus...
get_test_method: Get the test function name from the method name
load_peaks: Convert a BEDX+Y data.frame and into GRanges
num_peaks_per_gene: Aggregate peak assignments over the 'gene_id' column
plot_chipenrich_spline: QC plot for ChIP-Enrich
plot_dist_to_tss: Plot histogram of distance from peak to nearest TSS
plot_gene_coverage: QC plot for Broad-Enrich
plot_polyenrich_spline: QC plot for Poly-Enrich
polyenrich: Run Poly-Enrich on narrow genomic regions
post_process_enrichments: Post process the 'data.frame' of enrichment results
postprocess_peak_grs: A helper function to post-process peak GRanges
read_bed: Read files containing peaks or genomic regions
read_geneset: Function to read custom gene sets from file
read_ldef: Function to read custom locus definition from file
read_mappa: Function to read custom mappability files
recode_peaks: Recode a vector of number of peaks to binary based on...
reset_ncores_for_windows: Reset n_cores for Windows
setup_genesets: Function to setup genesets
setup_locusdef: Function to setup locus definitions
setup_mappa: Function to setup mappability
supported_genesets: Display supported genesets for gene set enrichment.
supported_genomes: Display supported genomes.
supported_locusdefs: Display supported locus definitions
supported_methods: Display supported gene set enrichment methods.
supported_read_lengths: Display supported read lengths for mappability

Functions

assign_peak_segments Man page Source code
assign_peaks Man page Source code
avg_binned_coverage Source code
avg_binned_numpeaks Source code
avg_binned_peak Source code
broadenrich Man page Source code
calc_approx_weights Source code
calc_peak_gene_overlap Man page Source code
calc_weights_chipenrich Source code
calc_weights_polyenrich Source code
chipenrich Man page Source code
chipenrich_package Man page
chipenrich_package-package Man page
filter_genesets Man page Source code
genome_to_organism Man page Source code
genome_to_orgdb Man page Source code
get_test_method Man page Source code
load_peaks Man page Source code
num_peaks_per_gene Man page Source code
peak_nearest_tss Source code
plot_chipenrich_spline Man page Source code Source code
plot_dist_to_tss Man page Source code Source code
plot_gene_coverage Man page Source code Source code
plot_polyenrich_spline Man page Source code Source code
polyenrich Man page Source code
post_process_enrichments Man page Source code
postprocess_peak_grs Man page Source code
randomize_ldef_bylength Source code
randomize_ldef_bylocation Source code
randomize_ldef_complete Source code
randomize_ppg_all Source code
randomize_ppg_length Source code
read_bed Man page Source code
read_geneset Man page Source code
read_ldef Man page Source code
read_mappa Man page Source code
recode_peaks Man page Source code
reset_ncores_for_windows Man page Source code
setup_genesets Man page Source code
setup_locusdef Man page Source code
setup_mappa Man page Source code
single_approx Source code
single_broadenrich Source code
single_chipenrich Source code
single_chipenrich_slow Source code
single_polyenrich Source code
single_polyenrich_slow Source code
supported_genesets Man page Source code
supported_genomes Man page Source code
supported_locusdefs Man page Source code
supported_methods Man page Source code
supported_read_lengths Man page Source code
test_approx Source code
test_binomial Source code
test_broadenrich Source code
test_broadenrich_splineless Source code
test_chipenrich Source code
test_chipenrich_slow Source code
test_fisher_exact Source code
test_polyenrich Source code
test_polyenrich_slow Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/assign_peaks.R
R/broadenrich.R
R/chipenrich.R
R/chipenrich_package_doc.R
R/constants.R
R/peaks_per_gene.R
R/plot_chipenrich_spline.R
R/plot_dist_to_tss.R
R/plot_gene_coverage.R
R/plot_polyenrich_spline.R
R/polyenrich.R
R/randomize.R
R/read.R
R/setup.R
R/supported.R
R/test_approx.R
R/test_binomial.R
R/test_broadenrich.R
R/test_chipenrich.R
R/test_chipenrich_slow.R
R/test_fisher.R
R/test_polyenrich.R
R/test_polyenrich_slow.R
R/utils.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/chipenrich-vignette.R
inst/doc/chipenrich-vignette.Rmd
inst/doc/chipenrich-vignette.html
inst/extdata
inst/extdata/test.bedGraph
inst/extdata/test.broadPeak
inst/extdata/test.broadPeak.gz
inst/extdata/test.gff3
inst/extdata/test.gff3.gz
inst/extdata/test.narrowPeak
inst/extdata/test.narrowPeak.gz
inst/extdata/test_assign.bed
inst/extdata/test_geneset.txt
inst/extdata/test_header.bed
inst/extdata/test_header.txt
inst/extdata/test_ldef_geneid.txt
inst/extdata/test_ldef_noextras.txt
inst/extdata/test_ldef_nosymbol.txt
inst/extdata/test_ldef_symbol.txt
inst/extdata/test_mappa_badhead.txt
inst/extdata/test_mappa_dup.txt
inst/extdata/test_mappa_good.txt
inst/extdata/test_mappa_neg.txt
inst/extdata/test_mappa_one.txt
inst/extdata/test_noheader.txt
inst/extdata/test_ppg.txt
inst/extdata/vignette_genesets.txt
man
man/assign_peak_segments.Rd
man/assign_peaks.Rd
man/broadenrich.Rd
man/calc_peak_gene_overlap.Rd
man/chipenrich.Rd
man/chipenrich_package.Rd
man/filter_genesets.Rd
man/genome_to_organism.Rd
man/genome_to_orgdb.Rd
man/get_test_method.Rd
man/load_peaks.Rd
man/num_peaks_per_gene.Rd
man/plot_chipenrich_spline.Rd
man/plot_dist_to_tss.Rd
man/plot_gene_coverage.Rd
man/plot_polyenrich_spline.Rd
man/polyenrich.Rd
man/post_process_enrichments.Rd
man/postprocess_peak_grs.Rd
man/read_bed.Rd
man/read_geneset.Rd
man/read_ldef.Rd
man/read_mappa.Rd
man/recode_peaks.Rd
man/reset_ncores_for_windows.Rd
man/setup_genesets.Rd
man/setup_locusdef.Rd
man/setup_mappa.Rd
man/supported_genesets.Rd
man/supported_genomes.Rd
man/supported_locusdefs.Rd
man/supported_methods.Rd
man/supported_read_lengths.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_0a_utils.R
tests/testthat/test_0b_setup.R
tests/testthat/test_0c_supported.R
tests/testthat/test_1_read.R
tests/testthat/test_2_assign_peaks.R
tests/testthat/test_3_peaks_per_gene.R
tests/testthat/test_4_randomize.R
tests/testthat/test_5_chipenrich.R
tests/testthat/test_6_qcplots.R
vignettes
vignettes/chipenrich-vignette.Rmd
chipenrich documentation built on May 20, 2017, 9:38 p.m.

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