iranges: base structures and functions not unlike memoryviews

The module reflects the content of the R/Bioconductor package IRanges. It defines Python-level classes for the R/S4 classes, and gives otherwise access to R-level commands the usual rpy2:robjects way.

The variable iranges_env in the module is an rpy2.robjects.REnvironment for the modules namespace. Accessing explicitly a module’s object is then straightforward.

The class inheritance diagram presents the parent-child relationships between the elements.

A module to model the IRanges library in Bioconductor

Copyright 2009 - Laurent Gautier

class bioc.iranges.AnnotatedList

class bioc.iranges.AtomicList

class bioc.iranges.CharacterList

class bioc.iranges.ComplexList

class bioc.iranges.CompressedAtomicList

class bioc.iranges.DataFrame

class bioc.iranges.IRanges

class bioc.iranges.IRangesList

class bioc.iranges.IntegerList

class bioc.iranges.IntervalTree

class bioc.iranges.LogicalList

class bioc.iranges.MaskCollection

get_width()

classmethod new(mask_width)

class bioc.iranges.NormalIRanges

max

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

min

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

class bioc.iranges.NumericList

class bioc.iranges.RangedData

end

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

get_names()

names

start

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

width

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

class bioc.iranges.Ranges

as_DataFrame()

as_integer()

as_matrix()

end

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

isdisjoint()

isempty()

isnormal()

mid()

start

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

whichfirst_notnormal()

width

Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.

class bioc.iranges.RangesDataList

class bioc.iranges.RangesList

class bioc.iranges.RawList

class bioc.iranges.Rle

class bioc.iranges.RleViews

class bioc.iranges.Sequence

Abstract class

class bioc.iranges.SimpleAtomicList

class bioc.iranges.SimpleList

class bioc.iranges.Views

get_subject()

Get the ‘subject’

subject

Get the ‘subject’

class bioc.iranges.XDataFrameList

class bioc.iranges.XRanges

bioc.iranges.iranges_conversion(robj)