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

 pval_specific_var R Documentation

## pval_specific_var

### Description

A function to retrieve a vector of p-values of each taxa for one specific variable. In other words, this will be useful for quickly accessing the taxa-specific p-values for main binary group variable (or other specific variable/covariate).

### Usage

``````pval_specific_var(pvaltab, varname)
``````

### Arguments

 `pvaltab` A table that includes p-values for a specific variable. `varname` Specify the name of the variable of interest.

### Value

A vector of p-values for a single variable from the model.

### 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 pval() function.
pvaltab <- pval(SOHPIEres)

# Retrieve a vector of p-values for a single variable of interest.
pval_specific_var(pvaltab = pvaltab, varname = "bin_dog")

``````

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