Calculate EMD score for a single gene
calculate_emd_gene(vec, outcomes, sample_names, binSize = 0.2)
A named vector containing data (e.g. expression data) for a single gene. Names ought to correspond to samples.
A vector of group labels for the samples. The names must correspond
to the names of
A character vector with the names of the samples in
The bin size to be used when generating histograms for each of the groups.
All possible combinations of the classes are used as pairwise comparisons.
The data in
vec is divided based on class labels based on the
identifiers given. For each pairwise computation, the
hist function is
used to generate histograms for the two groups. The densities are then retrieved
and passed to
emd2d to compute the pairwise EMD score. The
total EMD score for the given data is the average of the pairwise EMD scores.
The emd score is returned.
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# 100 genes, 100 samples dat <- matrix(rnorm(10000), nrow=100, ncol=100) rownames(dat) <- paste("gene", 1:100, sep="") colnames(dat) <- paste("sample", 1:100, sep="") # "A": first 50 samples; "B": next 30 samples; "C": final 20 samples outcomes <- c(rep("A",50), rep("B",30), rep("C",20)) names(outcomes) <- colnames(dat) calculate_emd_gene(dat[1,], outcomes, colnames(dat))
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