R: TaxaNorm Results

TaxaNorm_Results-class {TaxaNorm}

R Documentation

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)

[Package TaxaNorm version 2.4 Index]