Description Usage Arguments Value Examples
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.
1 | msc.matrix(files, samples, groups)
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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. |
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | 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
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