jointimpute: JointImpute: joint imputation method for microbiome data...

In lcw68/jointImpute: What the Package Does (One Line, Title Case)

Description

The function proposed an imputation method which output the imputed data as DNA and RNA level at the same time.

Usage

jointimpute(
  otu_dna,
  otu_rna,
  covariates_DNA,
  covariates_RNA,
  is_identify,
  epochs = 1,
  coef = 10000
)

Arguments

otu_dna	A m*n data frame/ matrix that represents OTU count table for DNA
otu_rna	A m*n data frame/ matrix that represents OTU count table for RNA
covariates_DNA	A n*p data frame/ matrix corresponding to covariates matrix/ meta data for DNA
covariates_RNA	A n*p data frame/ matrix corresponding to covariates matrix/ meta data for RNA
is_identify	indicator of whether we need identify step
epochs	Iteration times for imputation
coef	proportional constant for normalizing

Value

A list of imputed DNA and RNA matrix

Examples

covariates_DNA  <- data.frame(batch=factor(meta$batch.DNA), age=meta$age_mos, cariesfree=meta$cariesfree, reads=meta$reads.DNA/1e6)
covariates_RNA = data.frame(batch=factor(meta$batch.RNA),age=meta$age_mos,cariesfree=meta$cariesfree,reads = meta$reads.RNA/1e6)
otu_dna= otu[,,1]
otu_rna= otu[,,2]
otu.imp = jointimpute(otu_dna, otu_rna, covariates_DNA, covariates_RNA,is_identify = TRUE,epochs = 1)

lcw68/jointImpute documentation built on Dec. 21, 2021, 9:46 a.m.