msc.length: Length of minicircles

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

Description

The msc.length function allows you to check the length of minicircle sequences based on one fasta file.

Usage

msc.length(file, samples, groups)

Arguments

file	the name of the fasta file containing all minicircle sequences, e.g. all.minicircles.circ.fasta.
samples	a character vector containing the sample names.
groups	a vector, of equal length as samples, specifying to which group (e.g. subspecies) the samples belong to.

Value

length	a numerical vector containing the length of minicircle sequences.
plot	a histogram visualizing the length frequency of minicircle sequences.

Examples

require(ggplot2)
require(ggpubr)

### run function
bf <- msc.length(file = system.file("extdata", "all.minicircles.fasta", package="rKOMICS"),
                 samples = exData$samples, groups = exData$subspecies)
af <- msc.length(file = system.file("extdata", "all.minicircles.circ.fasta", package="rKOMICS"),
                 samples = exData$samples, groups = exData$subspecies)

length(which(bf$length<800)) 
length(which(bf$length>1400)) 

### visualize results
hist(af$length, breaks=50)

### alter plot
ggarrange(bf$plot + labs(caption = "Before filtering"), 
          af$plot + labs(caption = "After filtering"), nrow=2)

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