asso_mat {SOHPIE}

asso_mat

Description

A function to estimate an association matrix. This function also includes re-estimation for leave-one-out sample.

Usage

asso_mat(OTUdat, group)

Arguments

OTUdat

An OTU table with subjects in rows and taxa in columns.

group

Indices of the subjects in a category of binary group variable.

Value

A list of an association matrix and reestimated association matrix is returned, which are estimated via SparCC.

Examples

# In this example, the subset of the American Gut Project data will be used.
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]

# 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)

# Now, we estimate (and re-estimate) association matrices 
# for each group separately.
asso_matA = asso_mat(OTUdat=OTUtab, group=newindex_grpA) 
asso_matB = asso_mat(OTUdat=OTUtab, group=newindex_grpB)