calculate_emd_gene: Calculate EMD score for a single gene
In schmolze/emd: Earth Mover's Distance for Differential Analysis of Genomics Data

Description Usage Arguments Details Value See Also Examples

Calculate EMD score for a single gene

1	calculate_emd_gene(vec, samplesA, samplesB, binSize = 0.2)

`vec`	A named vector containing data (e.g. expression data) for a single gene.
`samplesA`	A vector of sample names identifying samples in `vec` that belong to "group A".
`samplesB`	A vector of sample names identifying samples in `vec` that belong to "group B".
`binSize`	The bin size to be used when generating histograms for "group A" and "group B".

The data in vec is divided into "group A" and "group B" by the identifiers given in samplesA and samplesB. The hist function is used to generate histograms for the two resulting groups, and the densities are retrieved and passed to emd2d to compute the EMD score.

The emd score is returned.

emd2d

# 100 samples
vec <- rnorm(100)
names(vec) <- paste("sample", 1:100, sep="")

# "group A" = first 50, "group B" = second 50
groupA <- names(vec)[1:50]
groupB <- names(vec)[51:100]

calculate_emd_gene(vec, groupA, groupB)