enve.df2dist.group {enveomics.R}

Enveomics: Data Frame to Dist (Group)

Description

Transform a dataframe (or coercible object, like a table) into a dist object, where there are 1 or more distances between each pair of objects.

Usage

enve.df2dist.group(
  x,
  obj1.index = 1,
  obj2.index = 2,
  dist.index = 3,
  summary = median,
  empty.rm = TRUE
)

Arguments

x

A dataframe (or coercible object) with at least three columns:

1. ID of the object 1,

2. ID of the object 2, and

3. 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.

summary

Function summarizing the different distances between the two objects.

empty.rm

Remove rows with empty or NA groups.

Value

Returns a dist object.

Author(s)

Luis M. Rodriguez-R [aut, cre]

Examples

# A sparse matrix representation of distances as data frame.
# Note that some pairs are repeated.
dist.df <- data.frame(
  query    = c("A", "A", "A", "B", "C", "C", "B", "B", "B"),
  subject  = c("A", "B", "C", "B", "C", "B", "A", "C", "C"),
  distance = c(  0, 0.1, 0.4,   0,   0, 0.4, 0.2, 0.2, 0.1)
)
dist <- enve.df2dist.group(dist.df)
print(dist)

# Use the mean of all repeated occurrences instead of the median.
dist <- enve.df2dist.group(dist.df, summary = mean)

# Simply use the first occurrence for any given pair.
dist <- enve.df2dist.group(dist.df, summary = function(x) head(x, n = 1))