SOHPIE (version 1.0.5)

qval_specific_var: qval_specific_var

Description

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

Usage

qval_specific_var(qvaltab, varname)

Value

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

Arguments

qvaltab

A table that includes q-values for a specific variable.

varname

Specify the name of the variable of interest.

Examples

# \donttest{
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)

# Create an object to keep the table with q-values using qval() function.
qvaltab <- qval(SOHPIEres)

# Retrieve a vector of q-values for a single variable of interest.
qval_specific_var(qvaltab = qvaltab, varname = "bin_dog")
# }