getSubset
Retrieve subset of elements from object
Description
uses additional options specified by one or more name-value pair arguments. For
example, you can specify whether to keep the data in memory. subset
= getSubset(object
,subset
,Name,Value
)
Examples
Retrieve Subset of Elements from NGS Data
Store read data from a SAM-formatted file in a BioRead
object. By default, the data remains in the source file, and BioRead
uses an index file to access the data, making the process more memory efficient.
br = BioRead('ex1.sam')
br = BioRead with properties: Quality: [1501x1 File indexed property] Sequence: [1501x1 File indexed property] Header: [1501x1 File indexed property] NSeqs: 1501 Name: ''
Set the 'InMemory'
name-value pair argument to true
to store the data in memory, enabling you to access the data faster and edit the properties of the object.
brInMemory = BioRead('ex1.sam','InMemory',true)
brInMemory = BioRead with properties: Quality: {1501x1 cell} Sequence: {1501x1 cell} Header: {1501x1 cell} NSeqs: 1501 Name: ''
Retrieve the second and third elements from the object br
. By default, the resulting object subset
is not placed in memory if the parent object br
is not in memory. If br
is already in memory, the resulting subset is placed in memory.
subset = getSubset(br,[2 3])
subset = BioRead with properties: Quality: [2x1 File indexed property] Sequence: [2x1 File indexed property] Header: [2x1 File indexed property] NSeqs: 2 Name: ''
Alternatively, you can keep the parent object br
in the source file, and load the resulting subset in memory if the subset is small enough. You access the subset faster and update it as needed.
subsetInMemory = getSubset(br,[2 3],'InMemory',true)
subsetInMemory = BioRead with properties: Quality: {2x1 cell} Sequence: {2x1 cell} Header: {2x1 cell} NSeqs: 2 Name: ''
Update the header information of the first element.
subsetInMemory.Header(1)
ans = 1x1 cell array
{'EAS54_65:7:152:368:113'}
subsetInMemory.Header(1) = {'NewHeader'};
subsetInMemory.Header(1)
ans = 1x1 cell array
{'NewHeader'}
You can use a header to get the corresponding elements with that header. If multiple elements have the same header, the function returns all those elements.
Get all the elements with the header 'B7_591:4:96:693:509'
from the br
object stored in memory.
subset2 = getSubset(brInMemory,{'B7_591:4:96:693:509'})
subset2 = BioRead with properties: Quality: {'<<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7'} Sequence: {'CACTAGTGGCTCATTGTAAATGTGTGGTTTAACTCG'} Header: {'B7_591:4:96:693:509'} NSeqs: 1 Name: ''
Input Arguments
subset
— Subset of elements in object
vector of positive integers | logical vector | string vector | cell array of character vectors
Subset of elements in the object, specified as a vector of positive integers, logical vector, string vector, or cell array of character vectors containing valid sequence headers.
Example: [1 3]
Tip
When you use a sequence header (or a cell array of headers) for subset
, a
repeated header specifies all elements with that header.
Name-Value Arguments
Specify optional pairs of arguments as
Name1=Value1,...,NameN=ValueN
, where Name
is
the argument name and Value
is the corresponding value.
Name-value arguments must appear after other arguments, but the order of the
pairs does not matter.
Before R2021a, use commas to separate each name and value, and enclose
Name
in quotes.
Example: 'InMemory',true
specifies to save the output object
(subset
) in memory.
Name
— Name of object
''
(default) | character vector | string
Name of the object, specified as the comma-separated pair consisting of
'Name'
and a character vector or string. The default is an empty
character vector ''
(no name).
Example: 'Name','newData'
InMemory
— Logical flag to keep data in memory
false
(default) | true
Logical flag to keep data in memory, specified as the comma-separated
pair consisting of 'InMemory'
and
true
or false
. Keeping the
data in memory lets you access the resulting object
subset
faster and update its properties. If the
data specified for subset
is still large and does
not fit in memory, set this name-value pair to false
to use indexed access, which is more memory efficient but does not
enable you to modify the properties.
If the parent object
is already in memory, the
resulting object subset
is automatically placed in
memory, and the function ignores this argument.
Example: 'InMemory',true
SelectReference
— References used to create subset of data
cell array of character vectors | string vector | vector of positive integers
References used to create the subset
of data with
only the reads mapped to those references, specified as the
comma-separated pair consisting of 'SelectReference'
and a cell array of character vectors, string vector, or vector of
positive integers.
Note
This argument is for the BioMap
objects
only.
Example: 'SelectReference',{'RefSeq1'}
Output Arguments
subset
— Subset of elements
BioRead
object | BioMap
object
Subset of elements from the object
, returned as a
BioRead
or BioMap
object. If
object
is in memory, then
subset
is placed in memory. If
object
is indexed, then subset
is indexed unless you set 'InMemory'
to
true
.
Version History
Introduced in R2010a
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