calculate_emd_gene: Calculate EMD score for a single gene

In EMDomics: Earth Mover's Distance for Differential Analysis of Genomics Data

Description

Calculate EMD score for a single gene

Usage

calculate_emd_gene(vec, outcomes, sample_names, binSize = 0.2)

Arguments

vec	A named vector containing data (e.g. expression data) for a single gene. Names ought to correspond to samples.
outcomes	A vector of group labels for the samples. The names must correspond to the names of vec.
sample_names	A character vector with the names of the samples in vec.
binSize	The bin size to be used when generating histograms for each of the groups.

Details

All possible combinations of the classes are used as pairwise comparisons. The data in vec is divided based on class labels based on the outcomes 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.

Value

The emd score is returned.

See Also

emd2d

Examples

# 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))

EMDomics documentation built on Nov. 8, 2020, 5:30 p.m.