getSubset

Create object containing subset of elements from BioIndexedFile object

Syntax

NewObj = getSubset(BioIFObj, Indices) NewObj = getSubset(BioIFObj, Keys)

Description

NewObj = getSubset(BioIFObj, Indices) returns NewObj, a new BioIndexedFile object that accesses a subset of entries in the source file associated with BioIFObj, a BioIndexedFile object. The entries are specified by Indices, a vector containing unique positive integers.

NewObj = getSubset(BioIFObj, Keys) returns NewObj, a new BioIndexedFile object that accesses a subset of entries in the source file associated with BioIFObj, a BioIndexedFile object. The entries are specified by Keys, a character vector or cell array of unique character vectors specifying keys.

Input Arguments

`BioIFObj`	Object of the `BioIndexedFile` class.
`Indices`	Vector containing unique positive integers that specify the entries in the source file to access with `NewObj`. The number of elements in `Indices` cannot exceed the number of entries indexed by `BioIFObj`. There is a one-to-one relationship between the elements in `Indices` and the entries that `NewObj` accesses.
`Keys`	Character vector or cell array of unique character vectors specifying keys that specify the entries in the source file to access with `NewObj`. The number of elements in `Keys` is less than or equal to the number of entries indexed by `BioIFObj`. If the keys in the source file are not unique, then all entries that match a given key are indexed by `NewObj`. In this case, there is not a one-to-one relationship between the elements in `Keys` and the entries that `NewObj` accesses. If the keys in the source file are unique, then there is a one-to-one relationship between the elements in `Keys` and the entries that `NewObj` accesses.

Output Arguments

NewObj

Object of the BioIndexedFile class.

Examples

Construct a BioIndexedFile object to access a table containing cross-references between gene names and gene ontology (GO) terms:

% Create a variable containing the full absolute path of the source file.
sourcefile = which('yeastgenes.sgd');
% Create a BioIndexedFile object from the source file. Indicate
% the source file is a tab-delimited file where contiguous rows
% with the same key are considered a single entry. Store the
% index file in the Current Folder. Indicate that keys are
% located in column 3 and that header lines are prefaced with !
gene2goObj = BioIndexedFile('mrtab', sourcefile, '.', ...
                            'KeyColumn', 3, 'HeaderPrefix','!')

Create a new BioIndexedFile object that accesses only the first 1,000 cross-references and reuses the same index file as gene2goObj:

% Create a new BioIndexedFile object.
gene2goSubset = getSubset(gene2goObj,1:1000);

Tips

Use this method to create a smaller, more manageable BioIndexedFile object.