abun_isometric_log_ratios: Compute isometric log ratio based on abundance of feature...

In POMS: Phylogenetic Organization of Metagenomic Signals

Compute isometric log ratio based on abundance of feature sets

Description

Computes isometric log ratio between two sets of feature abundances, for each sample separately. Requires an abundance table, with two sets of features for which the ratio will be computed.

Usage

abun_isometric_log_ratios(
  abun_table,
  set1_features,
  set2_features,
  pseudocount = NULL
)

Arguments

abun_table	Abundance table, e.g., read counts or relative abundance. Should be dataframe with column names correspond to sample names and row names corresponding to the feature ids. No 0's are permitted unless the "pseudocount" option is set.
set1_features	Features (rows of abundance table) that make up one side of the ratio to be computed (numerator).
set2_features	Same as "set1_features", but for the other side of the ratio (denominator).
pseudocount	Constant to add to all abundance values, to ensure that there are only non-zero values. For read count data this would typically be 1.

Value

Numeric vector of the computed isometric log ratio for each sample (where samples are taken to be each column in the input table).

POMS documentation built on Dec. 16, 2022, 5:08 p.m.