mcl: Run mcl.

In joelnitta/baitfindR: Find Baits for Sequence Capture

Description

This is a wrapper for the Markov Cluster Algorithm (mcl), a clustering algorithm for graphs. Here, it is meant to be used on genetic distances from BLAST.

Usage

mcl(mcl_input, mcl_output, i_value, e_value, other_args = NULL, ...)

Arguments

mcl_input	Character vector of length one; the path to the input file for mcl clustering.
mcl_output	Character vector of length one; the path to the output file produced by the mcl algorithm.
i_value	Numeric or character vector of length one; the inflation value.
e_value	Numeric or character vector of length one; the minimal -log transformed evalue to be considered by the algorithm.
other_args	Character vector; other arguments to pass to mcl. Each should be an element of the vector. For example, to pass "-abc" to specify the input file format and "–te" to specify number of threads, use c("--abc", "-te", "2").
...	Other arguments. Not used by this function, but meant to be used by drake_plan for tracking during workflows.

Value

A plain text file of tab-separated values, where each value on a line belongs to the same cluster.

Author(s)

Joel H Nitta, [e-mail]

References

Stijn van Dongen, A cluster algorithm for graphs. Technical Report INS-R0010, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, May 2000. https://micans.org/mcl/

Examples

## Not run: mcl(mcl_input = "some/folder/distance.file", mcl_output = "some/folder/mcl_output.txt", i_value = 1.4, evalue = 5)

joelnitta/baitfindR documentation built on May 7, 2020, 6:21 p.m.