Documentation

This is machine translation

Translated by Microsoft
Mouseover text to see original. Click the button below to return to the English verison of the page.

Note: This page has been translated by MathWorks. Please click here
To view all translated materals including this page, select Japan from the country navigator on the bottom of this page.

getSignature

Class: BioMap

Retrieve signature (alignment information) from BioMap object

Syntax

Signature = getSignature(BioObj)
Signature = getSignature(BioObj, Subset)

Description

Signature = getSignature(BioObj) returns Signature, a cell array of CIGAR-formatted strings, each representing how a read sequence in a BioMap object aligns to the reference sequence.

Signature = getSignature(BioObj, Subset) returns signature strings for only object elements specified by Subset.

Input Arguments

BioObj

Object of the BioMap class.

Subset

One of the following to specify a subset of the elements in BioObj:

  • Vector of positive integers

  • Logical vector

  • Cell array of character vectors containing valid sequence headers

Note

If you use a cell array of headers to specify Subset, be aware that a repeated header specifies all elements with that header.

Output Arguments

Signature

Signature property of a subset of elements in BioObj. Signature is a cell array of CIGAR-formatted strings, each representing how read sequences, specified by Subset, align to the reference sequence.

Examples

Construct a BioMap object, and then retrieve the signatures for different elements in the object:

% Construct a BioMap object from a SAM file 
BMObj1 = BioMap('ex1.sam');
% Retrieve the signature property of the second element in
% the object
Sig_2 = getSignature(BMObj1, 2)
Sig_2 = 

    '35M'
% Retrieve the signature properties of the first and third
% elements in the object
Sig_1_3 = getSignature(BMObj1, [1 3])
Sig_1_3 = 

    '36M'
    '35M'
% Retrieve the signature properties of all elements in the object
Sig_All = getSignature(BMObj1);

Alternatives

An alternative to using the getSignature method is to use dot indexing with the Signature property:

BioObj.Sgnature(Indices)

In the previous syntax, Indices is a vector of positive integers or a logical vector. Indices cannot be a cell array of character vectors containing sequence headers.

Was this topic helpful?