TaxaNorm_Results-class: TaxaNorm Results

In TaxaNorm: Feature-Wise Normalization for Microbiome Sequencing Data

TaxaNorm Results

Description

S4 class to store TaxaNorm Results

Usage

TaxaNorm_Results(
  input_data,
  rawdata,
  normdata,
  ecdf,
  model_pars,
  converge,
  llk,
  final_df
)

## S4 method for signature 'TaxaNorm_Results'
input_data(x)

## S4 replacement method for signature 'TaxaNorm_Results'
input_data(x) <- value

## S4 method for signature 'TaxaNorm_Results'
rawdata(x)

## S4 replacement method for signature 'TaxaNorm_Results'
rawdata(x) <- value

## S4 method for signature 'TaxaNorm_Results'
normdata(x)

## S4 replacement method for signature 'TaxaNorm_Results'
normdata(x) <- value

## S4 method for signature 'TaxaNorm_Results'
ecdf(x)

## S4 replacement method for signature 'TaxaNorm_Results'
ecdf(x) <- value

## S4 method for signature 'TaxaNorm_Results'
model_pars(x)

## S4 replacement method for signature 'TaxaNorm_Results'
model_pars(x) <- value

## S4 method for signature 'TaxaNorm_Results'
converge(x)

## S4 replacement method for signature 'TaxaNorm_Results'
converge(x) <- value

## S4 method for signature 'TaxaNorm_Results'
llk(x)

## S4 replacement method for signature 'TaxaNorm_Results'
llk(x) <- value

## S4 method for signature 'TaxaNorm_Results'
final_df(x)

## S4 replacement method for signature 'TaxaNorm_Results'
final_df(x) <- value

Arguments

input_data	passed to input_data slot
rawdata	Passed to rawdata slot
normdata	Passed to normdata slot
ecdf	Passed to ecdf slot
model_pars	Passed to model_pars slot
converge	Passed to converge slot
llk	Passed to llk slot
final_df	Passed to final_df slot
x	TaxaNorm_Results object
value	Replacement value

Details

All results from the TaxaNorm method and what was used to get those results

Functions

• input_data(TaxaNorm_Results): Return input_data slot

• rawdata(TaxaNorm_Results): Return rawdata slot

• normdata(TaxaNorm_Results): Return normdata slot

• ecdf(TaxaNorm_Results): Return ecdf slot

• model_pars(TaxaNorm_Results): Return model_pars slot

• converge(TaxaNorm_Results): Return converge slot

• llk(TaxaNorm_Results): Return llk slot

• final_df(TaxaNorm_Results): Return final_df slot

Slots

input_data

ANY phyloseq input data

rawdata

data.frame Data frame of counts to use

normdata

data.frame Normalized Data

ecdf

data.frame ecdf

model_pars

TaxaNorm_Model_Parameters list of model parameters

converge

⁠vector(<logical>)⁠ converge

llk

ANY llk

final_df

ANY final_df

Examples

coefficients <-  matrix(c(1,2,3,4,5,6,7,8,9),nrow=3,ncol=3,byrow=TRUE)
mu <- matrix(c(1,2,3,4,5,6,7,8,9),nrow=3,ncol=3,byrow=TRUE)
theta <-  matrix(c(1,2,3,4,5,6,7,8,9),nrow=3,ncol=3,byrow=TRUE)
pi <- matrix(c(1,2,3,4,5,6,7,8,9),nrow=3,ncol=3,byrow=TRUE)
model_pars <- TaxaNorm_Model_Parameters(coefficients = coefficients,mu = mu,theta = theta,pi = pi)
data("TaxaNorm_Example_Input", package = "TaxaNorm")
rawdata <- data.frame(Taxa1 = c(1,2,3),Taxa2 = c(3,4,5),Taxa3 = c(6,7,8))
normdata <- data.frame(Taxa1 = c(-1.4,-1.09,-0.73),
Taxa2 = c( -0.36,0,0.36), Taxa3 = c(0.73,1.09,1.46))
ecdf <- data.frame(0.05,0.23,0.89)
converge <- c(TRUE,TRUE,FALSE)
llk <- c(1,1.5,0.5)
final_df <- data.frame(Taxa1 = c(1,2,3),Taxa2 = c(3,4,5),Taxa3 = c(6,7,8))
TaxaNorm_Results(input_data = TaxaNorm_Example_Input,
                                  rawdata = rawdata,
                                   normdata = normdata,
                                   ecdf = ecdf,
                                   model_pars = model_pars,
                                   converge = converge,
                                   llk = llk,
                                   final_df = final_df)

TaxaNorm documentation built on June 24, 2024, 5:15 p.m.