Toolkit for Analysis of Genomic Data

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Documentation for package ‘misha’ version 5.4.5

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misha-package Toolkit for analysis of genomic data

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gbins.quantiles Calculates quantiles of a track expression for bins
gbins.summary Calculates summary statistics of a track expression for bins
gcis_decay Calculates distribution of contact distances
gcluster.run Runs R commands on a cluster
gcompute_strands_autocorr Computes auto-correlation between the strands for a file of mapped sequences
gcor Calculates correlation between track expressions
gdataset.example_path Create an example dataset on the fly
gdataset.info Get dataset information
gdataset.load Load a dataset into the namespace
gdataset.ls List working database and loaded datasets
gdataset.save Save a dataset
gdataset.unload Unload a dataset from the namespace
gdb.convert_to_indexed Change Database to Indexed Genome Format
gdb.create Creates a new Genomic Database
gdb.create_genome Create and Load a Genome Database
gdb.create_linked Create a linked database with symlinks to a parent database
gdb.export_fasta Export a database genome as FASTA
gdb.get_readonly_attrs Returns a list of read-only track attributes
gdb.info Get Database Information
gdb.init Initializes connection with Genomic Database
gdb.init.examples Initializes connection with Genomic Database
gdb.init_examples Initializes connection with Genomic Database
gdb.mark_cache_dirty Mark cached track list as dirty
gdb.reload Reloads database from the disk
gdb.set_readonly_attrs Sets read-only track attributes
gdir.cd Changes current working directory in Genomic Database
gdir.create Creates a new directory in Genomic Database
gdir.cwd Returns the current working directory in Genomic Database
gdir.rm Deletes a directory from Genomic Database
gdist Calculates distribution of track expressions
gextract Returns evaluated track expression
gintervals Creates a set of 1D intervals
gintervals.2d Creates a set of 2D intervals
gintervals.2d.all Returns 2D intervals that cover the whole genome
gintervals.2d.band_intersect Intersects two-dimensional intervals with a band
gintervals.2d.convert_to_indexed Convert 2D interval set to indexed format
gintervals.all Returns 1D intervals that cover the whole genome
gintervals.annotate Annotates 1D intervals using nearest neighbors
gintervals.as_chain Transforms existing intervals to a chain format
gintervals.canonic Converts intervals to canonic form
gintervals.chrom_sizes Returns number of intervals per chromosome
gintervals.convert_to_indexed Convert 1D interval set to indexed format
gintervals.coverage_fraction Calculate fraction of genomic space covered by intervals
gintervals.covered_bp Calculate total base pairs covered by intervals
gintervals.dataset Returns the database/dataset path for interval sets
gintervals.dbs Returns all database paths containing an interval set
gintervals.diff Calculates difference of two intervals sets
gintervals.exists Tests for a named intervals set existence
gintervals.force_range Limits intervals to chromosomal range
gintervals.import_genes Imports genes and annotations from files
gintervals.intersect Calculates an intersection of two sets of intervals
gintervals.is.bigset Tests for big intervals set
gintervals.liftover Converts intervals from another assembly
gintervals.load Loads a named intervals set
gintervals.load_chain Loads assembly conversion table from a chain file
gintervals.ls Returns a list of named intervals sets
gintervals.mapply Applies a function to values of track expressions
gintervals.mark_overlaps Mark overlapping intervals with a group ID
gintervals.neighbors Finds neighbors between two sets of intervals
gintervals.neighbors.directional Directional neighbor finding functions
gintervals.neighbors.downstream Directional neighbor finding functions
gintervals.neighbors.upstream Directional neighbor finding functions
gintervals.normalize Normalize intervals to fixed or variable sizes
gintervals.path Returns the path on disk of an interval set
gintervals.quantiles Calculates quantiles of a track expression for intervals
gintervals.random Generate random genome intervals
gintervals.rbind Combines several sets of intervals
gintervals.rm Deletes a named intervals set
gintervals.save Creates a named intervals set
gintervals.summary Calculates summary statistics of track expression for intervals
gintervals.union Calculates a union of two sets of intervals
gintervals.update Updates a named intervals set
giterator.cartesian_grid Creates a cartesian-grid iterator
giterator.intervals Returns iterator intervals
glookup Returns values from a lookup table based on track expression
gpartition Partitions the values of track expression
gquantiles Calculates quantiles of a track expression
grevcomp Get reverse complement of DNA sequence
gsample Returns samples from the values of track expression
gscreen Finds intervals that match track expression
gsegment Divides track expression into segments
gseq.comp Complement DNA sequence
gseq.extract Returns DNA sequences
gseq.kmer Score DNA sequences with a k-mer over a region of interest
gseq.kmer.dist Compute k-mer distribution in genomic intervals
gseq.pwm Score DNA sequences with a PWM over a region of interest
gseq.rev Reverse DNA sequence
gseq.revcomp Get reverse complement of DNA sequence
gsetroot Initializes connection with Genomic Database
gsummary Calculates summary statistics of track expression
gsynth.bin_map Create a bin mapping from value-based merge specifications
gsynth.load Load a gsynth.model from disk
gsynth.random Generate random genome sequences
gsynth.replace_kmer Iteratively replace a k-mer in the genome
gsynth.sample Sample a synthetic genome from a trained Markov model
gsynth.save Save a gsynth.model to disk
gsynth.train Train a stratified Markov-5 model from genome sequences
gtrack.2d.create Creates a 'Rectangles' track from intervals and values
gtrack.2d.import Creates a 2D track from tab-delimited file
gtrack.2d.import_contacts Creates a track from a file of inter-genomic contacts
gtrack.array.extract Returns values from 'Array' track
gtrack.array.get_colnames Returns column names of array track
gtrack.array.import Creates an array track from array tracks or files
gtrack.array.set_colnames Sets column names of array track
gtrack.attr.export Returns track attributes values
gtrack.attr.get Returns value of a track attribute
gtrack.attr.import Imports track attributes values
gtrack.attr.set Assigns value to a track attribute
gtrack.convert Converts a track to the most current format
gtrack.convert_to_indexed Convert a track to indexed format
gtrack.copy Copies a track
gtrack.create Creates a track from a track expression
gtrack.create_dense Creates a 'Dense' track from intervals and values
gtrack.create_dirs Create directories needed for track creation
gtrack.create_pwm_energy Creates a new track from PSSM energy function
gtrack.create_sparse Creates a 'Sparse' track from intervals and values
gtrack.dataset Returns the database/dataset path for a track
gtrack.dbs Returns the database paths that contain track(s)
gtrack.exists Tests for a track existence
gtrack.import Creates a track from WIG / BigWig / BedGraph / BED / tab-delimited file
gtrack.import_mappedseq Creates a track from a file of mapped sequences
gtrack.import_set Creates one or more tracks from multiple WIG / BigWig / BedGraph / tab-delimited files on disk or FTP
gtrack.info Returns information about a track
gtrack.liftover Imports a track from another assembly
gtrack.lookup Creates a new track from a lookup table based on track expression
gtrack.ls Returns a list of track names
gtrack.modify Modifies track contents
gtrack.mv Renames or moves a track
gtrack.path Returns the path on disk of a track
gtrack.rm Deletes a track
gtrack.smooth Creates a new track from smoothed values of track expression
gtrack.var.get Returns value of a track variable
gtrack.var.ls Returns a list of track variables for a track
gtrack.var.rm Deletes a track variable
gtrack.var.set Assigns value to a track variable
gvtrack.array.slice Defines rules for a single value calculation of a virtual 'Array' track
gvtrack.create Creates a new virtual track
gvtrack.filter Attach or clear a genomic mask filter on a virtual track
gvtrack.info Returns the definition of a virtual track
gvtrack.iterator Defines modification rules for a one-dimensional iterator in a virtual track
gvtrack.iterator.2d Defines modification rules for a two-dimensional iterator in a virtual track
gvtrack.ls Returns a list of virtual track names
gvtrack.rm Deletes a virtual track
gwget Downloads files from FTP server
gwilcox Calculates Wilcoxon test on sliding windows over track expression

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misha Toolkit for analysis of genomic data

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print.gsynth.model Print summary of a gsynth.model