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plotPerPositionGC

Class: BioReadQualityStatistics

Plot percentages of G or C nucleotides at each base position

Syntax

plotPerPositionGC(QSObj)
H = plotPerPositionGC(QSObj)

Description

plotPerPositionGC(QSObj) generates a line plot displaying the percentages of G or C nucleotides at each base position for the BioReadQualityStatistics object QSObj.

H = plotPerPositionGC(QSObj) returns the handle H to the axes object containing the generated plot.

Input Arguments

QSObj

BioReadQualityStatistics object.

Output Arguments

H

Handle to axes object containing generated plot.

Examples

expand all

Create a BioReadQualityStatistics object from a FASTQ file using only the first 40 characters of each read with a minimum average quality score of 5.

QSObj = BioReadQualityStatistics('SRR005164_1_50.fastq', ...
                                  'FilterLength', 40, ...
                                  'QualityScoreThreshold', 5);

Plot percentages of G or C nucleotide at each base position.

plotPerPositionGC(QSObj)
ans = 

  Axes (GC Content) with properties:

             XLim: [0.1000 41]
             YLim: [0 100]
           XScale: 'linear'
           YScale: 'linear'
    GridLineStyle: '-'
         Position: [0.1300 0.1100 0.7750 0.8150]
            Units: 'normalized'

  Use GET to show all properties

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