SOHPIE (version 1.0.5)

asso_mat: 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)

Value

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

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.

Examples

# \donttest{
# 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) 

# }