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setReference

Class: BioMap

Set name of reference sequence for BioMap object

Syntax

newObj = setReference(Obj,RefSeqName)
newObj = setReference(Obj,RefSeqName,Indices)

Description

newObj = setReference(Obj,RefSeqName) returns a new BioMap object newObj, constructed from an existing object Obj, with the Reference property set to RefSeqName, a character vector specifying the name of the reference sequence.

newObj = setReference(Obj,RefSeqName,Indices) sets the Reference property of the elements indexed by Indices to RefSeqName.

Input Arguments

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Object of the BioMap class, specified as a BioMap object.

Name of reference sequence, specified as a character vector or cell array of character vectors.

Indices to the elements of the input object, specified as a positive integer, vector of positive integers, logical array, character vector, or cell array of character vectors. For character vectors, they must correspond to the valid Header values of the input object Obj.

Output Arguments

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Object of the BioMap class, returned as a BioMap object.

Examples

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Create a BioMap object from a SAM file. Set 'InMemory' to true to allow modifying the object properties.

bm = BioMap('ex2.sam','InMemory',true);

Check the reference sequence of the 5th read sequence.

bm.Reference(5)
ans =

  cell

    'seq1'

Change the reference sequence to another one in the sequence dictionary.

bm2 = setReference(bm,{'seq2'},5);
bm2.Reference(5)
ans =

  cell

    'seq2'

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