bioinfo.pipeline.block.CuffQuant

Bioinformatics pipeline block to quantify gene and transcript expression profiles

Since R2023a

• 

Description

A CuffQuant block enables you to quantify gene and transcript expression profiles by generating abundance estimates for the samples.

The block requires the Cufflinks Support Package for the Bioinformatics Toolbox™. If the support package is not installed, then a download link is provided. For details, see Bioinformatics Toolbox Software Support Packages.

Creation

Syntax

b = bioinfo.pipeline.block.CuffQuant

b = bioinfo.pipeline.block.CuffQuant(options)

b = bioinfo.pipeline.block.CuffQuant(Name=Value)

Description

b = bioinfo.pipeline.block.CuffQuant creates a CuffQuant block.

b = bioinfo.pipeline.block.CuffQuant(options) also specifies additional options.

b = bioinfo.pipeline.block.CuffQuant(Name=Value) specifies additional options as the property names and values of a CuffQuantOptions object. This object is set as the value of the Options property of the block.

Input Arguments

options — CuffQuant options

CuffQuantOptions | string | character vector

CuffQuant options, specified as a CuffQuantOptions object, string, or character vector.

If you are specifying a string or character vector, it must be in the CuffQuant native syntax (prefixed by one or two dashes) [1].

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Note

The following list of arguments is a partial list. For the complete list, refer to the properties of CuffQuantOptions object.

EffectiveLengthCorrection — Flag to normalize fragment counts

true (default) | false

Flag to normalize fragment counts to fragments per kilobase per million mapped reads (FPKM), specified as true or false.

Example: false

Data Types: logical

ExtraCommand — Additional commands

"" (default) | string | character vector

The commands must be in the native syntax (prefixed by one or two dashes). Use this option to apply undocumented flags and flags without corresponding MATLAB^® properties.

When the software converts the original flags to MATLAB properties, it stores any unrecognized flags in this property.

Example: '--library-type fr-secondstrand'

Data Types: char | string

Properties

ErrorHandler — Function to handle errors from run method

function handle

Function to handle errors from the run method of the block, specified as a function handle. The handle specifies the function to call if the run method encounters an error within a pipeline. For the pipeline to continue after a block fails, ErrorHandler must return a structure that is compatible with the output ports of the block. The error handling function is called with the following two inputs:

• Structure with these fields:

  Field	Description
  identifier	Identifier of the error that occurred
  message	Text of the error message
  index	Linear index indicating which block process failed in the parallel run. By default, the index is 1 because there is only one run per block. For details on how block inputs can be split across different dimensions for multiple run calls, see Bioinformatics Pipeline SplitDimension.

• Input structure passed to the run method when it fails

Data Types: function_handle

Inputs — Input ports

structure

This property is read-only.

Input ports of the block, specified as a structure. The field names of the structure are the names of the block input ports, and the field values are bioinfo.pipeline.Input objects. These objects describe the input port behaviors. The input port names are the expected field names of the input structure that you pass to the block run method.

The CuffQuant block Inputs structure has the following fields:

• GenomicAnnotationFile — Name of the transcript annotation file. The file can be a GTF or GFF file produced by Cufflinks, CuffCompare, or another source of GTF annotations. This input is a required input that must be satisfied.

• GenomicAlignmentFiles — Names of SAM or BAM files containing alignment records for each sample. This input is a required input that must be satisfied.

The default value for each input field is a bioinfo.pipeline.datatypes.Unset object, which means that the input value is not set yet.

Data Types: struct

Outputs — Output ports

structure

This property is read-only.

Output ports of the block, specified as a structure. The field names of the structure are the names of the block output ports, and the field values are bioinfo.pipeline.Output objects. These objects describe the output port behaviors. The field names of the output structure returned by the block run method are the same as the output port names.

The CuffQuant block Outputs structure has the following field:

• CXBFile — Name of the abundances file.

Tip

To see the actual location of the output file, first get the results of the block. Then use the unwrap method as shown in this example.

Data Types: struct

Options — CuffQuant options

CuffQuantOptions object (default)

CuffQuant options, specified as a CuffQuantOptions object. The default value is a default CuffQuantOptions object.

Object Functions

compile	Perform block-specific additional checks and validations
copy	Copy array of handle objects
emptyInputs	Create input structure for use with run method
eval	Evaluate block object
run	Run block object

Examples

Use CuffQuant Block to Quantify Transcript Expressions

Calculate abundances (expression levels) from aligned reads for samples using CuffQuant.

import bioinfo.pipeline.block.*
import bioinfo.pipeline.Pipeline

FC1 = FileChooser(which("gyrAB.gtf"));
samFiles = {which("Myco_1_1.sam"),which("Myco_1_2.sam")};
FC2 = FileChooser(samFiles);
CQ = CuffQuant;

P = Pipeline;
addBlock(P,[FC1,FC2,CQ]);
connect(P,FC1,CQ,["Files","GenomicAnnotationFile"]);
connect(P,FC2,CQ,["Files","GenomicAlignmentFiles"]);

run(P);
R = results(P,CQ)

R = 

  struct with fields:

    CXBFile: [1×1 bioinfo.pipeline.datatypes.File]

Call unwrap on the field of the result structure R.

unwrap(R.CXBFile)

ans = 

    "C:\PipelineResults\CuffQuant_1\1\abundances.cxb"

References

[1] Trapnell, Cole, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, and Lior Pachter. “Transcript Assembly and Quantification by RNA-Seq Reveals Unannotated Transcripts and Isoform Switching during Cell Differentiation.” Nature Biotechnology 28, no. 5 (May 2010): 511–15.

Version History

Introduced in R2023a