KallistoExperiment-class: A SummarizedExperiment subclass that stores multiple Kallisto...

In RamsinghLab/arkas_staging: A package that complements Kallisto for quick, informative *seq analysis

Description

A SummarizedExperiment subclass that stores multiple Kallisto runs

returns the estimated counts of a quantified experiment

returns the phenotypic data associated with a KallistoExperiment object

a replacement function specific to phenotypic data

finds the effective length of a transcript entry

finds the transcript per million

finds the kallistoVersion used in quantification

finds the transcriptomes pseudo-aligned against

median abs deviation

Usage

## S4 method for signature 'KallistoExperiment'
counts(object)

## S4 method for signature 'KallistoExperiment'
pData(object)

## S4 replacement method for signature 'KallistoExperiment,DataFrame'
pData(object) <- value

eff_length(object)

## S4 method for signature 'KallistoExperiment'
eff_length(object)

tpm(object)

## S4 method for signature 'KallistoExperiment'
tpm(object)

kallistoVersion(object)

## S4 method for signature 'KallistoExperiment'
kallistoVersion(object)

transcriptomes(object)

## S4 method for signature 'KallistoExperiment'
transcriptomes(object)

mabDev(object)

## S4 method for signature 'KallistoExperiment'
mabDev(object)

Arguments

object	KallistoExperiment
value	this is the replacement value for object

Slots

transcriptomes

Transcriptomes against which reads were pseudoaligned

kallistoVersion

The version of Kallisto used to pseudoalign the reads

Slots

transcriptomes:

character class "character", containing data from transcriptomes

kallistoVersion:

Object of class "character", containing data that needs to go in kallistoVersion.

RamsinghLab/arkas_staging documentation built on March 14, 2021, 11:40 a.m.