R: Calculate permutations and derived stats abundance count data

sample_matrix {KbaseKit}

R Documentation

Calculate permutations and derived stats abundance count data

Description

This function calculates permutations and derived stats abundance count data.

Usage

sample_matrix(file_name, num_perm = 1, perm_type = "sample_rand", write_files = FALSE, perm_dir = "./permutations/", verbose = FALSE, debug = FALSE)

Arguments

`file_name`	Required name or path/name of file to process
`num_perm`	Number of permutations to perform
`perm_type`	Type of permutations: either `"sample_rand"`, `"dataset_rand"`, or `"complete_rand"`
`write_files`	Whether to write a file for each permutation / iteration
`perm_dir`	Directory for permutation files
`verbose`	Whether to print verbose output to `stdout`
`debug`	Whether to print debug output to `stdout`

Details

"sample_rand" shuffles values among fields within a sample / column (dataset distribution is maintained, as is the distribution for each sample / column); "dataset_rand" shuffles fields within the entire data set (maintaining total counts and the original data set distribution); "complete_rand" randomly distributes sum of counts about an equally sized matrix (maintaining total counts, but not distribution).

Value

Returns zero on success.

Author(s)

Kevin Keegan

Examples

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[Package KbaseKit version 0.9 Index]