msc.uc: Cluster Analyses

Description Usage Arguments Value Examples

View source: R/msc.uc.R

Description

The msc.uc function allows you to check some clustering : insertions and deletions –> ask Fre. The total amount of minicircle sequence clusters (MSCs) found per percent identity will be calculated as well as the number of gaps.

Usage

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Arguments

files

a character vector containing the uc file names (output of VSEARCH) e.g. all.minicircles.circ.id70.uc, all.minicircles.circ.id80.uc...

Value

MSCs

a numerical vector containing the number of MSC per percent identity.

perfect aligments

a numerical vector containing the proportions of perfect alignments per percent identity.

insertions

a table showing the length and the number of insertions across different percent identities.

deletions

a table showing the length and the number of deletions across different percent identities.

plots

different plots showing previous results.

Examples

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data(exData)

### run function

ucs <- msc.uc(files = system.file("extdata", exData$ucs, package="rKOMICS"))

ucs$MSCs["100"] 
ucs$MSCs["97"] 

### results
ucs$plots

rKOMICS documentation built on July 21, 2021, 5:07 p.m.