EzAppCountOverlaps-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 ezMethodCountOverlaps(input=NA, output=NA, param=NA)()

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

• ezMethodCountOverlaps(input=NA, output=NA, param=NA) : The function to run this application.

• countNonredundant(bamFile, param=param, gff=gff): Counts the non-redundant overlaps.

• countBamHitsSingleChrom(chr, bamFile=NULL, param=NULL, gff=NULL): Counts the BAM hits for a single chromosome.

• countPairedBamHitsSingleChrom(chr, bamFile=NULL, param=NULL, gff=NULL): Counts the paired BAM hits for a single chromosome.

• getTargetRanges(gff, param, chrom=NULL): Gets the target ranges depending on param$featureLevel.

• getFeatureCounts(chrom, gff, reads, param): Gets the feature counts from the target ranges.

Author(s)

Rehrauer, Hubert

Schmid, Peter

See Also

EzApp

EzDataset

uzh/ezRun documentation built on April 19, 2024, 8:25 a.m.