epiG: DNA methylation and SNP calling for bisulfite sequencing data
Version 1.0.0

DNA methylation and SNP calling for bisulfite sequencing data.

AuthorMartin Vincent
Date of publication2015-05-22 10:05:07
MaintainerMartin Vincent <vincent@math.ku.dk>
LicenseGPL (>= 2)
Version1.0.0
URL
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("epiG", repos="http://R-Forge.R-project.org")

Popular man pages

chain.info: chain.info
create_error_distributions: create_error_distributions
fetch_alt: fetch_alt
fetch.reads: fetch_reads
genotype: genotype
genotype.epiG: genotype codeing C = 1, G = 2, A = 3, T = 4
strand.epiG: strand
See all...

All man pages Function index File listing

Man pages

chain.info: chain.info
chain.info.epiG: chain.info
compute_chunk_positions: Compute chunk positions
coverage: coverage
coverage.epiG: coverage
create_bisulfite_model: create_bisulfite_model
create_error_distributions: create_error_distributions
create_genotype_prior_alt: create_genotype_prior_alt
create_genotype_prior_ref: create_genotype_prior
end: end position
end.epiG: end
epiG: Fit an epiG model
epiG.algorithm.config: Create a epiG configuration
epiG.chunks: epiG.chunks
exp_decay: exp_decay
fetch_alt: fetch_alt
fetch.reads: fetch_reads
fetch_reads_info: fetch_reads_info
fetch_ref: fetch_ref
genotype: genotype
genotype.epiG: genotype codeing C = 1, G = 2, A = 3, T = 4
length.epiG: Length of model in base pairs
locate.DGCH: locate DGCH positions
locate.GCH: locate GCH positions
locate.HCGD: locate HCGD positions
locate.SNP: locate SNP positions
methylation: methylation
methylation.epiG: methylation
nchain: Number of chains
nchain.epiG: Number of chains
nchunks: Number of chunks
nchunks.epiG: Number of chunks
nread: Number of reads in model
nread.epiG: Number of reads in model
position.info: position.info
position.info.epiG: position.info
print.epiG: print
print.epiG.config: print config
read.fasta: Read fasta
read.info: read.info
read.info.epiG: read.info
start: start position
start.epiG: start
strand: strand
strand.epiG: strand
subregion: subregion
subregion.epiG: subregion
symbols: symbols
vector.search: vector search

Functions

chain.info Man page Source code
chain.info.epiG Man page Source code
compute_chunk_positions Man page Source code
coverage Man page Source code
coverage.epiG Man page Source code
create_bisulfite_model Man page Source code
create_error_distributions Man page Source code
create_genotype_prior_alt Man page Source code
create_genotype_prior_ref Man page Source code
end Man page Source code
end.epiG Man page Source code
epiG Man page Source code
epiG.algorithm.config Man page Source code
epiG.chunks Man page Source code
exp_decay Man page Source code
fetch.reads Man page Source code
fetch_alt Man page Source code
fetch_reads_info Man page Source code
fetch_ref Man page Source code
genotype Man page Source code
genotype.epiG Man page Source code
length.epiG Man page Source code
locate.DGCH Man page Source code
locate.GCH Man page Source code
locate.HCGD Man page Source code
locate.SNP Man page Source code
methylation Man page Source code
methylation.epiG Man page Source code
nchain Man page Source code
nchain.epiG Man page Source code
nchunks Man page Source code
nchunks.epiG Man page Source code
nread Man page Source code
nread.epiG Man page Source code
position.info Man page Source code
position.info.epiG Man page Source code
print.epiG Man page Source code
print.epiG.config Man page Source code
read.fasta Man page Source code
read.info Man page Source code
read.info.epiG Man page Source code
start Man page Source code
start.epiG Man page Source code
strand Man page Source code
strand.epiG Man page Source code
subregion Man page Source code
subregion.epiG Man page Source code
symbols Man page Source code
vector.search Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/epiG_config.R
R/epiG_fetch.R
R/epiG_haplo_fit.R
R/epiG_locate.R
R/epiG_navigate.R
R/epiG_summary.R
man
man/chain.info.Rd
man/chain.info.epiG.Rd
man/compute_chunk_positions.Rd
man/coverage.Rd
man/coverage.epiG.Rd
man/create_bisulfite_model.Rd
man/create_error_distributions.Rd
man/create_genotype_prior_alt.Rd
man/create_genotype_prior_ref.Rd
man/end.Rd
man/end.epiG.Rd
man/epiG.Rd
man/epiG.algorithm.config.Rd
man/epiG.chunks.Rd
man/exp_decay.Rd
man/fetch.reads.Rd
man/fetch_alt.Rd
man/fetch_reads_info.Rd
man/fetch_ref.Rd
man/genotype.Rd
man/genotype.epiG.Rd
man/length.epiG.Rd
man/locate.DGCH.Rd
man/locate.GCH.Rd
man/locate.HCGD.Rd
man/locate.SNP.Rd
man/methylation.Rd
man/methylation.epiG.Rd
man/nchain.Rd
man/nchain.epiG.Rd
man/nchunks.Rd
man/nchunks.epiG.Rd
man/nread.Rd
man/nread.epiG.Rd
man/position.info.Rd
man/position.info.epiG.Rd
man/print.epiG.Rd
man/print.epiG.config.Rd
man/read.fasta.Rd
man/read.info.Rd
man/read.info.epiG.Rd
man/start.Rd
man/start.epiG.Rd
man/strand.Rd
man/strand.epiG.Rd
man/subregion.Rd
man/subregion.epiG.Rd
man/symbols.Rd
man/vector.search.Rd
src
src/Makevars
src/alignment_data.h
src/arma_additions.h
src/bam_reader.h
src/chain_opt.h
src/chunked_chain_opt.h
src/epiG.cpp
src/epiG_algorithm_config.h
src/genotype_opt.h
src/math_tools.h
src/prior.h
src/rinterface
src/rinterface/epiG.h
src/rinterface/fetch.h
src/rtools
src/rtools.h
src/rtools/get_value.h
src/rtools/omp_rwarnings.h
src/rtools/rList.h
src/rtools/rObject_decl.h
src/rtools/rObject_def.h
src/samtools
src/samtools/LICENSE
src/samtools/bam.c
src/samtools/bam.h
src/samtools/bam_aux.c
src/samtools/bam_endian.h
src/samtools/bam_import.c
src/samtools/bam_index.c
src/samtools/bam_sort.c
src/samtools/bgzf.c
src/samtools/bgzf.h
src/samtools/faidx.c
src/samtools/faidx.h
src/samtools/khash.h
src/samtools/kseq.h
src/samtools/ksort.h
src/samtools/kstring.c
src/samtools/kstring.h
src/samtools/razf.c
src/samtools/razf.h
src/samtools/sam.c
src/samtools/sam.h
src/samtools/sam_header.c
src/samtools/sam_header.h
src/seq_tools.h
src/simple_timer.h
src/types.h
src/vector_search.h
epiG documentation built on May 21, 2017, 4:07 a.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.