jaccardInd: Compute Jaccard index

In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

Compute Jaccard index

Description

Compute Jaccard index

Usage

jaccardInd(list1, list2, universeSize, pvalue = FALSE, indexSignif = 2,
  pvalSig = 3, figure = FALSE, Col = c("coral4", "darkorchid1"),
  categories, condition, policeFont = "Linux Libertine", saveFile = NA,
  outputType = "index", ...)

Arguments

list1	vector of gene names from a first element to compare
list2	vector of genes names from a second element to compare
universeSize	positive integer. Number of elements in the universe
pvalue	boolean. Default: FALSE. Whether a p-value should be computed
indexSignif	positive integer. Default: 2. Number of significant digits to add for the Jaccard index on the figure.
pvalSig	positive integer. Default: 3. Number of significant digits to add for the p-value on the figure.
figure	boolean. default: FALSE. Whether a figure showing the overlap should be displayed
Col	Colour palette: vector of two character strings. Colours to use to draw the two elements being compared in the venn diagram
categories	vector of two character strings that are the names of the two elements being compared.
condition	character string. Name of the condition compared between the two elements.
policeFont	character string. Name of the font to use.
saveFile	path (character string). Default: NA. Allows to save the figure (if figure=TRUE) at the given path.
outputType	character string. Whether "index" to return the Jaccard index; "pval" for the p-value associated or "list" for a list comprising the index and the pvalue, "intersect" intersection of the two lists.
...	other parameters for grDevices::cairo_pdf

Value

depends on outputType. Refer to that argument for the possible output.

barzine/barzinePhdR documentation built on Nov. 23, 2024, 8:54 p.m.