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genoset (version 1.28.2)

A RangedSummarizedExperiment with methods for copy number analysis

Description

GenoSet provides an extension of the RangedSummarizedExperiment class with additional API features. This class provides convenient and fast methods for working with segmented genomic data. Additionally, GenoSet provides the class RleDataFrame which stores runs of data along the genome for multiple samples and provides very fast summaries of arbitrary row sets (regions of the genome).

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Version

Version

1.28.2

License

Artistic-2.0

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Repository

https://github.com/phaverty/genoset

Maintainer

Peter M Haverty

Last Published

February 15th, 2017

Functions in genoset (1.28.2)

Calculate GC Percentage in sliding window

Get base positions of features in genome-scale units

Center continuous data on mode

Convert Rle objects to tables of segments

rangeSegMeanLength

Get segment widths

Get list of unique chromosome names

nrow,GenomicRanges-method

GenomicRanges API Additions

Calculate mBAF from BAF

Plot data along the genome

Calculate GC Percentage in windows

[,GenoSet,ANY-method

Subset a GenoSet

Count Rle positions >= min

.do_rledf_views

Calculate min/max/sum/mean/whichmin/whichmax over each view on each column of an RleDataFrame.

boundingIndices

Find indices of features bounding a set of chromosome ranges/genes

Make Rle from segments for one sample

Set a GRanges or GenoSet to genome order

Get a matrix of first and last index of features in each chromosome

Check if a GRanges orGenoSet is in genome order

Load a GenoSet from a RData file

Convert bounding indices into a Rle

Correct copy number for GC content

Take vector or matrix of copynumber values, convert to log2ratios

Create a GenoSet object

chrPartitioning

Partitioning by Chromosome

Get and set the genome universe annotation.

Get chromosome start and stop positions

Class "GenoSet"

RleDataFrame-class

Class "RleDataFrame"

segs2RleDataFrame

CBS segments to probe matrix

Fix NA runs in a Rle

Run CBS Segmentation

Chromosome name for each feature

rangeSampleMeans

Average features in ranges per sample

Take vector or matrix of log2 ratios, convert to copynumber

RleDataFrame-views

Calculate summary statistics on views of an RleDataFrame

genoset-datasets

Example GenoSet object

boundingIndicesByChr

Find indices of features bounding a set of chromosome ranges/genes, across chromosomes

Order chromosome names in proper genome order

A fast method for concatenating data.frames

GRanges from segment table

Chromosome position of features

genoset-package

GenoSet: An eSet for data with genome locations

Label axis with base pair units

Convert Rle objects to tables of segments

.do_rledf_range_summary

Calculate min/max/sum/mean/whichmin/whichmax over ranges on each column of an RleDataFrame.