enve.df2dist: Enveomics: Data Frame to Dist

In enveomics.R: Various Utilities for Microbial Genomics and Metagenomics

Enveomics: Data Frame to Dist

Description

Transform a dataframe (or coercible object, like a table) into a dist object.

Usage

enve.df2dist(
  x,
  obj1.index = 1,
  obj2.index = 2,
  dist.index = 3,
  default.d = NA,
  max.sim = 0
)

Arguments

x	A dataframe (or coercible object) with at least three columns: ID of the object 1, ID of the object 2, and distance between the two objects.
obj1.index	Index of the column containing the ID of the object 1.
obj2.index	Index of the column containing the ID of the object 2.
dist.index	Index of the column containing the distance.
default.d	Default value (for missing values).
max.sim	If not zero, assumes that the values are similarity (not distance) and this is the maximum similarity (corresponding to distance 0). Applies transformation: distance = (max.sim - values)/max.sim.

Value

Returns a dist object.

Author(s)

Luis M. Rodriguez-R [aut, cre]

Examples

# A sparse matrix representation of similarities as data frame.
# The column "extra_data" is meaningless, only included to illustrate
# the use of the obj*.index parameters
sim <- data.frame(
  extra_data = c(0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.5),
  query      = c("A", "A", "A", "B", "C", "C", "D"),
  subject    = c("A", "B", "C", "B", "C", "B", "A"),
  similarity = c(100,  90,  60, 100, 100,  70,  10)
)
dist <- enve.df2dist(sim, "query", "subject", "similarity", max.sim = 100)
print(dist)

enveomics.R documentation built on April 13, 2022, 5:10 p.m.