msc.uc: Cluster Analyses

In GeertsManon/rKOMICS: Minicircle Sequence Cluster (MSC) Analyses

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

msc.uc(files)

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

data(exData)

### run function

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

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

### results
ucs$plots

GeertsManon/rKOMICS documentation built on Dec. 17, 2021, 9:28 p.m.