genome_content_phylo_regress {POMS}

Phylogenetic regression of input vector against function presence/absence.

Description

Runs phylogenetic regression with phylolm on each function (or trait) in the specified function table.

Usage

genome_content_phylo_regress(y, func, in_tree, ncores = 1, model_type = "BM")

Arguments

y

variable to use for y component of model. Typically would be either a binary vector indicating which taxa are significantly different, or the normalized specicity or normalized prevalence values. Must be a named numeric vector with names matching the rows of the func dataframe. These names also must match the tree tip labels, but they can be a subset and any missing tips will be dropped.

func

dataframe of the number of copies of each function that are encoded by each input taxon. This pipeline only considers the presence/absence of functions across taxa. Taxa (with row names intersecting with the "abun" table) should be the rows and the functions should be the columns.

in_tree

phylo object. Tip labels must include the row names of the func dataframe and the names of the y input vector.

ncores

integer specifying how many cores to use for parallelized sections of pipeline.

model_type

length-one character vector specifying which phylogenetic model to use (must be a possible setting of the model argument to the phylolm function).

Value

Dataframe summarizing the phylolm coefficients and model p-values for each y ~ function comparison. Will include the intercept, slope, and p-value for each case. Row names will be function ids.