EzAppFastqc-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 ezMethodFastQC(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

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

• plotReadCountToLibConc(dataset, colname): Plots colname from dataset against read counts in millions.

• getQualityMatrix(inputFile): Gets a quality count matrix from a fastq or gziped fastq.gz file with dimensions read quality and read length.

• plotQualityMatrixAsHeatmap(qualMatrixList, isR2=FALSE, xScale=1, yScale=1): Returns a png table of quality matrices interpreted as heatmaps.

• plotQualityHeatmap(result, name=NULL, colorRange=c(0,sqrt(40)), colors=gray((1:256)/256), main=NULL, pngFileName=NULL, xScale=1, yScale=1): Creates and returns the images used by plotQualityMatrixAsHeatmap().

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

EzApp

EzDataset

uzh/ezRun documentation built on March 5, 2025, 3:41 p.m.