qpcrImpute: Impute Non-detects in qPCR data

Description Usage Arguments Value Author(s) Examples

View source: R/qpcrImpute.R

Description

This function models the missing data mechanism and uses an EM algorithm to impute the non-detect values in qPCR data.

Usage

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qpcrImpute(object, dj=NULL, pyfit=NULL, groupVars=NULL, 
          batch=NULL, tol=1, iterMax=100, 
          outform=c("Single","Param","Multy"), 
          vary_fit=TRUE, vary_model=TRUE, add_noise=TRUE, 
          formula=NULL, numsam=5, 
          linkglm = c("logit", "probit", "cloglog"))

Arguments

object

a qPCRset

dj

normalization values. If NULL, features with "control" in featureType(object) are used to normalize the data. If no control features are found, the data are not normalized.

pyfit

initial estimate of the relationship between the probability of a non-detect and average expression. If NULL, this relationship is estimated from the data.

groupVars

which columns in pData(object) should be used to determine replicate samples. If NULL, all columns are used.

batch

amatrix with control samples for each batch, if NULL, batch effect is not taken into account.

tol

likelihood convergence criterion of the EM algorithm.

iterMax

maximimum number of iterations of the EM algorithm.

outform

the form of the output requested.If "Single" performes a single imputation of missing values. If "Param" returnes estimated model parameters: mean and variance. If "Multy" performes a multiple imputation of missing values, and creats multiple data sets with imputed values.

vary_fit

if outform="Multy", includes the model uncertainty due to the logit of the probability of being missing. The default value is "TRUE".

vary_model

if outform="Multy", includes the model uncertainty due to the estimating mean of the data. The default value is "TRUE".

add_noise

if outform="Multy", introduses the variance component due to the random noise. The default value is "TRUE".

formula

specifies the model.

numsam

number of the datasets to be created if outform="Multy". The default value is 5.

linkglm

a link used for estimation of the missing data mechanism.

Value

The function returns a qPCRset object with non-detects replaced by their imputed values.

Author(s)

Valeriia Sherina

Examples

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  data(sagmb2011)
  tst <- qpcrImpute(sagmb2011, groupVars="sampleType",
                    outform=c("Single"), batch=NULL, linkglm = c("logit"))

valery-sherina/nondetects_devel documentation built on May 29, 2019, 11:57 a.m.