EzAppFastqScreen-class: The R5 class representing a runnable app using...

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

The R5 class representing a runnable app using ezMethodFastqScreen(input=NA, output=NA, param=NA, htmlFile="00index.html")()

Description

Use this reference class to run

Arguments

input	a list, file path or an object of the class EzDataset containing the input.
output	a list, file path or an object of the class EzDataset containing the output information.
param	a list of parameters to customize the application run.

Fields

runMethod

the function that will be executed in the run method.

name

the name of the application.

appDefaults

the defaults to run the application with.

Methods

initialize()

Initializes the application using its specific defaults.

Functions

• ezMethodFastqScreen(input=NA, output=NA, param=NA, htmlFile="00index.html") : The function to run this application.

• executeFastqscreenCMD(param, files): Executes the fastqscreen command with given parameters on the input files.

• collectFastqscreenOutput(dataset, files, resultFiles): Collects the fastqscreen output after the result files have been obtained by executeFastqscreenCMD().

• executeBowtie2CMD(param, input): Executes the bowtie2 command with given parameters on the input files.

• collectBowtie2Output(param, dataset, countFiles): Collects the bowtie2 output after the count files have been obtained by executeBowtie2CMD().

• fastqscreenReport(dataset, param, htmlFile="00index.html", fastqData, speciesPercentageTop): Generates a report with plots and other information about the outcome of the run.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

EzApp

EzDataset

uzh/ezRun documentation built on Sept. 16, 2024, 11:21 p.m.