pval: pval

In SOHPIE: Statistical Approach via Pseudo-Value Information and Estimation

pval

Description

A function to retrieve a vector of p-values of each taxa for all variables that are included in the pseudo-value regression model.

Usage

pval(SOHPIEres)

Arguments

SOHPIEres

An object called after running SOHPIE_DNA.

Value

A table that includes p-values for all predictor variables considered in the regresson.

Examples

data(combinedamgut) # A complete data containing columns with taxa and clinical covariates.

# Note: The line below will use a toy example with the first 30 out of 138 taxa.
OTUtab = combinedamgut[ , 8:37]
# Clinical/demographic covariates (phenotypic data):
# Note: All of these covariates will be included in the regression, so
# please make sure that phenodat includes the variables that will be analyzed only.
phenodat = combinedamgut[, 1:7] # first column is ID, so not using it.
# Obtain indices of each grouping factor
# In this example, a variable indicating the status of living with a dog was chosen (i.e. bin_dog).
# Accordingly, Groups A and B imply living without and with a dog, respectively.
 newindex_grpA = which(combinedamgut$bin_dog == 0)
 newindex_grpB = which(combinedamgut$bin_dog == 1)

SOHPIEres <- SOHPIE_DNA(OTUdat = OTUtab, clindat = phenodat,
groupA = newindex_grpA, groupB = newindex_grpB, c = 0.5)

# Create an object to keep the table with p-values using qval() function.
pvaltab <- pval(SOHPIEres)

SOHPIE documentation built on Oct. 24, 2023, 1:06 a.m.