Toolkit for analysis of genomic data

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Documentation for package ‘misha’ version 4.0.6

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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.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.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-dimenstional 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
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
gset_input_mode Sets input mode and auto-completion for track expressions, track names, virtual tracks and interval sets
gsummary Calculates summary statistics of track expression
gtraceback Prints call stack of the last uncaught error
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_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