Epiviz

Class: GenomicRanges

GenomicRanges

new epiviz.datatypes.deprecated.GenomicRanges(id, seqindex, start, end, strand, values, levels)

datatypes/deprecated/genomic-ranges.js, line 25

A collection of genomic ranges

.

A collection of genomic ranges

Name Type Description
id Array.<string> optional
seqindex Array.<number> | number optional
start Array.<number> optional
end Array.<number> optional
strand Array.<string> | string optional
values Object.<string, Array> optional
levels Array.<string> optional
Deprecated
  • Yes

Classes

Hits

Overlap hits resulted from a findOverlaps operation over two GenomicRanges instances

.
Row
Subset

Members

staticepiviz.datatypes.deprecated.GenomicRanges.TYPEstring

A constant denoting the type name

.

A constant denoting the type name

Methods

staticepiviz.datatypes.deprecated.GenomicRanges.createQuery(seqinfo, start, end){epiviz.datatypes.deprecated.GenomicRanges}

datatypes/deprecated/genomic-ranges.js, line 111
Name Type Description
seqinfo epiviz.datatypes.deprecated.SeqInfo
start number
end number
Returns:
Type Description
epiviz.datatypes.deprecated.GenomicRanges

staticepiviz.datatypes.deprecated.GenomicRanges.fromRawObject(o){epiviz.datatypes.deprecated.GenomicRanges}

datatypes/deprecated/genomic-ranges.js, line 100
Name Type Description
o Object

A parsed JSON object containing raw data for the genomic ranges. Subfields: id: an array of string values for the ids of each genomic range seqindex: an array of chromosome numbers for each range, corresponding to indices in the levels array; can also contain a single value, in which case all ranges are assumed to belong to the same chromosome. start: an array of start base pairs for the ranges end: an array of end base pairs for the ranges strand: an array of strings corresponding to the direction of the strand of each range; if instead of an array there's one single value, then all ranges are assumed to belong to the same strand. values: a map of column names as keys and arrays as values, containing metadata for the genomic range; this field is optional. levels: an array of names for all chromosomes in the instance; the numbers in seqindex correspond to indices in this array
Returns:
Type Description
epiviz.datatypes.deprecated.GenomicRanges

staticepiviz.datatypes.deprecated.GenomicRanges.merge(gr1, gr2){epiviz.datatypes.deprecated.GenomicRanges}

datatypes/deprecated/genomic-ranges.js, line 252

Merges two genomic ranges instances together by location, eliminating common rows (where ids match) TODO: Consider creating a wrapper class for the result of this function, which simply maps indices, without performing a hard copy

.

Merges two genomic ranges instances together by location, eliminating common rows (where ids match) TODO: Consider creating a wrapper class for the result of this function, which simply maps indices, without performing a hard copy

Name Type Description
gr1 epiviz.datatypes.deprecated.GenomicRanges
gr2 epiviz.datatypes.deprecated.GenomicRanges
Returns:
Type Description
epiviz.datatypes.deprecated.GenomicRanges

protected_initializeIntervalForest()

datatypes/deprecated/genomic-ranges.js, line 118

dataType(){string}

datatypes/deprecated/genomic-ranges.js, line 140
Returns:
Type Description
string

end(index){number}

datatypes/deprecated/genomic-ranges.js, line 367
Name Type Description
index number
Returns:
Type Description
number

findOverlaps(query){epiviz.datatypes.deprecated.GenomicRanges.Hits}

datatypes/deprecated/genomic-ranges.js, line 183
Name Type Description
query epiviz.datatypes.deprecated.GenomicRanges
Returns:
Type Description
epiviz.datatypes.deprecated.GenomicRanges.Hits

foreach(fun)

datatypes/deprecated/genomic-ranges.js, line 163

Iterates through all genomic ranges until fun returns something that evaluates to true

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Iterates through all genomic ranges until fun returns something that evaluates to true

Name Type Description
fun function

get(i){epiviz.datatypes.deprecated.GenomicRanges.Row}

datatypes/deprecated/genomic-ranges.js, line 153
Name Type Description
i number

a numeric index of the row
Returns:
Type Description
epiviz.datatypes.deprecated.GenomicRanges.Row

id(index){string}

datatypes/deprecated/genomic-ranges.js, line 340
Name Type Description
index number
Returns:
Type Description
string

levels(){Array.<string>}

datatypes/deprecated/genomic-ranges.js, line 392
Returns:
Type Description
Array.<string>

ranges(){epiviz.datatypes.deprecated.GenomicRanges}

datatypes/deprecated/genomic-ranges.js, line 147
Returns:
Type Description
epiviz.datatypes.deprecated.GenomicRanges

seqinfo(index){epiviz.datatypes.deprecated.SeqInfo}

datatypes/deprecated/genomic-ranges.js, line 349
Name Type Description
index number
Returns:
Type Description
epiviz.datatypes.deprecated.SeqInfo

size(){number}

datatypes/deprecated/genomic-ranges.js, line 175
Returns:
Type Description
number the total number of rows in the structure

start(index){number}

datatypes/deprecated/genomic-ranges.js, line 359
Name Type Description
index number
Returns:
Type Description
number

strand(index){string}

datatypes/deprecated/genomic-ranges.js, line 375
Name Type Description
index number
Returns:
Type Description
string

subsetByOverlaps(query){epiviz.datatypes.deprecated.GenomicRanges}

datatypes/deprecated/genomic-ranges.js, line 240
Name Type Description
query
Returns:
Type Description
epiviz.datatypes.deprecated.GenomicRanges

value(column, index){*}

datatypes/deprecated/genomic-ranges.js, line 384
Name Type Description
column string
index number
Returns:
Type Description
*

valueColumns(){Array.<string>}

datatypes/deprecated/genomic-ranges.js, line 328
Returns:
Type Description
Array.<string> the names of the value columns associated with the epiviz.datatypes.deprecated.GenomicRanges instance
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