getQuality

Retrieve sequence quality information from object

Syntax

quality = getQuality(object)

subsetQuality = getQuality(object,subset)

Description

quality = getQuality(object) returns sequence quality information from a BioRead or BioMap object.

subsetQuality = getQuality(object,subset) returns the sequence quality information subsetQuality for only the object elements specified by subset.

Examples

Retrieve Sequence Quality Information

Store read data from a SAM-formatted file in a BioRead object.

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: ''

Retrieve sequence quality information.

seqQuals = getQuality(br);

Retrieve sequence quality information from the first and third elements in the object.

seqQuals2 = getQuality(br,[1 3])

seqQuals2 = 2x1 cell
    {'<<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7'}
    {'<<<<<<<<<<<7;71<<;<;;<7;<<3;);3*8/5' }

Use a logical vector to get the same information.

seqQuals3 = getQuality(br,[true false true])

seqQuals3 = 2x1 cell
    {'<<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7'}
    {'<<<<<<<<<<<7;71<<;<;;<7;<<3;);3*8/5' }

You can use a header to get the quality of the corresponding sequence with that header. If multiple sequences have the same header, the function returns the quality information of all those sequences.

Get the quality information of the sequences with the header B7_591:4:96:693:509.

seqQuals4 = getQuality(br,{'B7_591:4:96:693:509'})

seqQuals4 = 1x1 cell array
    {'<<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7'}

Access each property of the object using the dot notation.

seqQuals = br.Quality;
seqQuals2   = br.Quality([1 3])

seqQuals2 = 2x1 cell
    {'<<<<<<<<<<<<<<<;<<<<<<<<<5<<<<<;:<;7'}
    {'<<<<<<<<<<<7;71<<;<;;<7;<<3;);3*8/5' }

Input Arguments

object — Object containing read data

BioRead object | BioMap object

Object containing the read data, specified as a BioRead or BioMap object.

Example: bioreadObj

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.

Output Arguments

quality — Sequence quality information

cell array of character vectors

Sequence quality information, returned as a cell array of character vectors. Each character is an ASCII-encoded value of the log probability of a base being incorrect.

subsetQuality — Sequence quality information for subset of elements

cell array of character vectors

Sequence quality information for a subset of elements from the object, returned as a cell array of character vectors.

Version History

Introduced in R2010a