Description Usage Arguments Value Examples
The msc.subset allows you to find specific MSC for a certain subset of samples.
1 | msc.subset(clustmatrix, subset)
|
clustmatrix |
a cluster matrix |
subset |
a numerical vector indicating which subset of samples to include. |
clustnumbers |
a vector containing the specific MSC names. |
freq |
frequency values of those specific MSC in the subset of samples. |
matrix |
a subset of the cluster matrix containing only those specific MSC. All samples, not in the subset, should have a value of 0 meaning the MSC is absent. |
sum |
the total number of MSC found in the indicated subset of samples. |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | data(matrices)
data(exData)
### selecting a group of samples e.g. all L. peruviana species
Lpe <- which(exData$species == "L. peruviana")
### run function
specific <- msc.subset(matrices[["id97"]], subset = Lpe)
### visualize results (check if it is indeed specific)
heatmap(specific$matrix) # or:
msc.heatmap(specific$matrix, samples = exData$samples, groups = exData$species)
### find specific MSC with highest frequency
which.max(specific$freq)
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