msc.matrix: Build cluster matrix

In rKOMICS: Minicircle Sequence Cluster (MSC) Analyses

Description

Clustering based on a percent identity, performed with the VSEARCH tool, will generate files in uc format. The msc.matrix function will transform every input file into a cluster matrix. The columns of the matrix correspond to the samples and the rows of the matrix correspond to the minicircle sequence cluster (MSC). The absence of a MSC in a sample is indicated with the value of zero while the presence of a MSC in a sample will be indicated with a value >= 1.

Usage

msc.matrix(files, samples, groups)

Arguments

files	a character vector containing the uc file names (output of the VSEARCH tool) e.g. all.minicircles.circ.id70.uc, all.minicircles.circ.id80.uc...
samples	a character vector containing the sample names. The vector should be order alphabetically.
groups	a vector, of equal length as samples, specifying to which group (e.g. species) the samples belong to.

Value

a list containing one cluster matrix per percent identity. The value 0 in the cluster matrix means the MSC doesn't occur in the sample. A value higher than 0 means the MSC is found at least once in the sample.

Examples

data(exData)

### run function

matrices <- msc.matrix(files = system.file("extdata", exData$ucs, package="rKOMICS"), 
                      samples = sort(exData$samples), 
                      groups = exData$species[order(exData$samples)])


### or: 
data(matrices)

### show matrix with id 95%
matrices[["id95"]]
rowSums(matrices[["id95"]]) # --> frequency of MSC across all samples
colSums(matrices[["id95"]]) # --> number of MSC per sample

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