getSummary

Class: BioMap

Print summary of BioMap object

Syntax

getSummary(BioObj)
ds = getSummary(BioObj)


Description

getSummary(BioObj) prints a summary of a BioMap object. The summary includes the names of references, the number of sequences mapped to each reference, and the genomic range that the sequences cover in each reference.

ds = getSummary(BioObj) returns the summary information in a dataset array.

Input Arguments

BioObj

Object of the BioMap class.

Output Arguments

ds

dataset array containing the summary of the BioMap object, BioObj. The dataset array has an observation (row) for each reference in BioObj, and two variables (columns): the number of sequences mapped to each reference and the genomic range that the sequences cover in each reference. getSummary stores additional metadata for the BioMap object in the UserData property of ds, which you can access using ds.Properties.UserData.

Examples

Construct a BioMap object, and then display a summary of the object:

% Construct a BioMap object from a SAM file 
BMObj2 = BioMap('ex2.sam');
getSummary(BMObj2)

BioMap summary:
                                  Name: ''
                        Container_Type: 'Data is file indexed.'
             Total_Number_of_Sequences: 3307
    Number_of_References_in_Dictionary: 2

            Number_of_Sequences    Genomic_Range
    seq1    1501                   1  1569      
    seq2    1806                   1  1567