clustur (version 0.1.2)

read_dist: Read distance matrices

Description

Read in distances from a file that is formatted with three columns for the row, column, and distance of a sparse, square matrix or in a phylip-formatted distance matrix.

Usage

read_dist(distance_file, count_table, cutoff, is_similarity_matrix = FALSE)

Value

A distance `externalptr` object that contains all your distance information. Can be accessed using `get_distance_df()`

Arguments

distance_file

Either a phylip or column distance file, or a sparse matrix. The function will detect the format for you.

count_table

A table of names and the given abundance per group. Can be in mothur's sparse or full format. The function will detect the format for you.

cutoff

The value you wish to use as a cutoff when clustering.

is_similarity_matrix

are you using a similarity matrix (default) or distance matrix?

Examples

 i_values <- as.integer(1:100)
 j_values <- as.integer(sample(1:100, 100, TRUE))
 x_values <- as.numeric(runif(100, 0, 1))
 s_matrix <- create_sparse_matrix(i_values, j_values, x_values)

 sparse_count <- data.frame(
                 Representative_Sequence = 1:100,
                 total = rep(1, times = 100))

 column_path <- example_path("amazon_column.dist")
 phylip_path <- example_path("amazon_phylip.dist")
 count_table <- read_count(example_path("amazon.full.count_table"))

 data_column <- read_dist(column_path, count_table, 0.03)
 data_phylip <- read_dist(phylip_path, count_table, 0.03)
 data_sparse <- read_dist(s_matrix, sparse_count, 0.03)