startCompDTUReg: 'startCompDTUReg' start the compositional DTU regression...

In skvanburen/CompDTUReg: CompDTUReg: Fit Compositional Regression Models for DTU

startCompDTUReg start the compositional DTU regression model corresponding to a specific gene-level file.

Description

startCompDTUReg runs the compositional DTU regression models. This is a helper function to run CompDTUReg from gene level files originating from the file (4)RunCompositionalRegressions.R in the sample code for the package.

Usage

startCompDTUReg(
  x,
  runWithME,
  customHypTest = FALSE,
  NullDesign = NULL,
  AltDesign = NULL
)

Arguments

x	The file path to a specific gene-level file
runWithME	is TRUE/FALSE indicating whether the model should be run with measurement error or not (corresponding to CompDTU and CompDTUme models respectively). If runWithME is TRUE ensure YInfRep is non-NULL and if runWithME is FALSE ensure Y is non-NULL.
customHypTest	should be set to TRUE if custom design matrices will be specified using the NullDesign and AltDesign arguments. If TRUE the Group argument must be set to NULL. Default is FALSE.
NullDesign	specifies the design matrix corresponding to the null hypothesis if a custom hypothesis test is specified via customHypTest being set to TRUE. Number of rows needs to be the number of samples, even if CompDTUme is to be run (the matrix will be replicated automatically as needed).
AltDesign	specifies the design matrix corresponding to the alternative hypothesis if a custom hypothesis test is specified via customHypTest being set to TRUE. Number of rows needs to be the number of samples, even if CompDTUme is to be run (the matrix will be replicated automatically as needed).

Details

This function loads results from SaveGeneLevelFiles that contain all input arguments aside from any custom specified design matrices, and input arguments to CompDTUReg are automatically set by startCompDTUReg. See the file (4)RunCompositionalRegressions.R in the package's SampleCode folder for example code.

Value

a data.frame containing the gene_id being used, p-value from the CompDTU or CompDTUme significance test for condition, and various information on the current dataset being used.

skvanburen/CompDTUReg documentation built on Jan. 23, 2025, 9:01 a.m.