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getEntryByIndex

Class: BioIndexedFile

Retrieve entries from source file associated with BioIndexedFile object using numeric index

Syntax

Entries = getEntryByIndex(BioIFobj, Indices)

Description

Entries = getEntryByIndex(BioIFobj, Indices) extracts entries from the source file associated with BioIFobj, a BioIndexedFile object. It extracts and concatenates the entries specified by Indices, a numeric vector of positive integers. It returns Entries, a character vector of concatenated entries. The value of each element in Indices must be less than or equal to the number of entries in the source file. A one-to-one relationship exists between the number and order of elements in Indices and the output Entries, even if Indices has repeated entries.

Input Arguments

BioIFobj

Object of the BioIndexedFile class.

Indices

Numeric vector of positive integers. The value of each element must be less than or equal to the number of entries in the source file associated with BioIFobj, the BioIndexedFile object.

Output Arguments

Entries

Character vector of concatenated entries extracted from the source file associated with BioIFobj, the BioIndexedFile object.

Examples

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

% Create variable containing full absolute path of 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','!')

Return the first, third, and fifth entries from the source file:

% Access 1st, 3rd, and 5th entries
subset_entries = getEntryByIndex(gene2goObj, [1 3 5]);

Tips

Use this method to visualize and explore a subset of the entries in the source file for validation purposes.

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