plotSummary

Class: BioRead

Plot summary statistics of BioRead object

Syntax

plotSummary(BRObj)
plotSummary(BRObj,Name,Value)
[H,qsObj] = plotSummary(___)

Description

plotSummary(BRObj) generates a summary statistics figure containing six plots about the average quality score for each base position, average quality score distribution, read count percentage for each base position, percentage of GC content for each base position, GC content distribution, and nucleotide distribution.

plotSummary(BRObj,Name,Value) generates a summary statistics figure using additional options specified by one or more name-value pair arguments.

[H,qsObj] = plotSummary(___) returns a column vector H of handles to the axes in the generated figure and a BioReadQualityStatistics object qsObj using any of the input arguments from the previous syntaxes.

Input Arguments

BRObj

BioRead or BioMap object.

Name-Value Pair Arguments

'Encoding'

String specifying the format used for the characters encoding the sequence information and quality scores in a sequence file. Supported formats are 'Sanger', 'Illumina13', 'Illumina15', 'Illumina18', and 'Solexa'.

Default: 'Illumina18'

'FilterLength'

Positive integer (n) specifying the first n characters of each read to be used. Use an empty array to supress filtering.

Default: []

'QualityScoreThreshold'

Scalar value specifying a minimum average quality threshold for a read to be considered. Any read with an average score of less than the specified threshold value is ignored. The default value is –Inf, which causes all reads to be considered.

Default: -Inf

    Note:   If 'FilterLength' is set to L and 'QualityScoreThreshold' is set to T, then a read is discarded if the average quality of the first L characters of the read is less than T.

Output Arguments

H

Column vector of handles to the axes in the generated figure.

qsObj

BioReadQualityStatistics object that stores the data represented by the graphs.

Examples

Plot Summary Statistics of BioRead Object

Create a BioRead object from a FASTQ file.

BRObj = BioRead('SRR005164_1_50.fastq');

Plot summary statistics of the BioRead object BRObj using the first 40 characters of each read with the minimum average quality score of 5.

plotSummary(BRObj,'FilterLength',40,'QualityScoreThreshold',5)

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