Toolkit for Analysis of Genomic Data

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Documentation for package ‘misha’ version 4.3.6

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

Help Pages

misha-package	Toolkit for analysis of genomic data
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
gdb.create	Creates a new Genomic Database
gdb.create_genome	Create and Load a Genome Database
gdb.get_readonly_attrs	Returns a list of read-only track attributes
gdb.init	Initializes connection with Genomic Database
gdb.init.examples	Initializes connection with Genomic Database
gdb.init_examples	Initializes connection with Genomic Database
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.all	Returns 1D intervals that cover the whole genome
gintervals.canonic	Converts intervals to canonic form
gintervals.chrom_sizes	Returns number of intervals per chromosome
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.neighbors	Finds neighbors between two sets of intervals
gintervals.quantiles	Calculates quantiles of a track expression for 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.extract	Returns DNA sequences
gsetroot	Initializes connection with Genomic Database
gsummary	Calculates summary statistics of track expression
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.create	Creates a track from a track expression
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.exists	Tests for a track existence
gtrack.import	Creates a track from WIG / BigWig / BedGraph / 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.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.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
misha	Toolkit for analysis of genomic data