View source: R/coeff_specific_var.R

coeff_specific_var | R Documentation |

A function to retrieve a vector of coefficient estimates of each taxa for one specific variable.

```
coeff_specific_var(coefftab, varname)
```

`coefftab` |
A table that includes coefficient estimates for a specific variable. |

`varname` |
Specify the name of the variable of interest. |

A vector of coefficient estimates for a single variable from the model.

```
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)
# coeff() function will return coefficient estimates only.
coefftab <- coeff(SOHPIEres)
# coeff_specific_var() will return coefficient estimates of
# a single variable of interest.
coeff_specific_var(coefftab = coefftab, varname = "bin_dog")
```

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