iDAS_3F.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/threeway_functions.R
\name{iDAS_3F}
\alias{iDAS_3F}
\title{Interpretable differential abundance analysis (three-way analysis)}
\usage{
iDAS_3F(
  Z,
  f1,
  f2,
  f3,
  random = NULL,
  test_func = "lm",
  Sig_cutoff = 0.02,
  Sig = 0.05,
  Int = 0.01,
  F1 = 0.01,
  F2 = 0.01,
  F3 = 0.01,
  F1F2 = 0.01,
  F1F3 = 0.01,
  F2F3 = 0.01,
  threeways = 0.01,
  adj_method = "BH",
  f1name = NULL,
  f2name = NULL,
  f3name = NULL,
  randomname = NULL
)
}
\arguments{
\item{Z}{A matrix/dataframe of omics or gene expression data, row as sample.}

\item{f1}{A vector of factor 1 variables.}

\item{f2}{A vector of factor 2 variables.}

\item{f3}{A vector of factor 3 variables.}

\item{random}{A vector of random effect term of ANOVA analysis,
by default is NULL, which means the model doesn't include random effect term.}

\item{test_func}{Testing function used, either stats::lm or lme4::lmer. By default is "lm".}

\item{Sig_cutoff}{No effect test significance level is defined by a fraction value
to indicate when ordering the p-values
and defining the top X\% as the significance level. If both Sig_cutoff and Sig
are set, the algorithm will, by default, use Sig_cutoff to determine
the significance level.}

\item{Sig}{No effect test significance level is defined directly
by a fraction value, by default is 0.05}

\item{Int}{Interaction effect test significance level,by default is 0.01}

\item{F1}{Factor 1 effect test significance level, by default is 0.01}

\item{F2}{Factor 2 effect test significance level, by default is 0.01}

\item{F3}{Factor 3 effect test significance level, by default is 0.01}

\item{F1F2}{F1 and F2 interaction effect test significance level, by default is 0.01}

\item{F1F3}{F1 and F3 interaction effect test significance level, by default is 0.01}

\item{F2F3}{F2 and F3 interaction effect test significance level, by default is 0.01}

\item{threeways}{three-way effect test significance level, by default is 0.01}

\item{adj_method}{Pvalue adjust method. See p.adjust. By default is "BH".}

\item{f1name}{The column name of factor 1, by default is F1.}

\item{f2name}{The column name of factor 2, by default is F2.}

\item{f3name}{The column name of factor 3, by default is F3.}

\item{randomname}{The column name of random effect term, by default is Random.}
}
\value{
A list of hypothesis test outcome, P_mat is the pvalue matrix of all tests,
S_mat is the statistics matrix of all test, cls_df is the Classification data frame of all tests.
}
\description{
This function will be no longer be used.
}
\examples{
#res=iDAS_3F(Z = X,
#f1 = all.timepoint, f2 = all.pcellstats, f3 = all.pcelltype, random = all.pid, test_func = "lmer",
#Sig_cutoff = 0.02,Int = 0.01,F1 = 0.01,F2=0.02,F3=0.01,adj_method = "BH")
}
\keyword{internal}