tissuesDistance: Compute the distance between the tissues within a study.

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

Compute the distance between the tissues within a study.

Description

the distance is based on the number of genes that are uniquely shared by a number of given tissues only.

Usage

tissuesDistance(DF, nbOfTissues = 2, ColN, gid = FALSE, plot = FALSE,
  method = "ward.D", notecol = "gray37",
  col = colorRampPalette(c("aliceblue", "darkcyan")), threshold = 0,
  ...)

Arguments

DF	numeric data.frame that contains
nbOfTissues	integer (>0) number of tissues in which the genes have to be expressed to be considered
ColN	vector of character strings. Names of the tissues to include in the analysis.
gid	boolean. Default: FALSE. Whether to output the name of the concerned genes instead of their number.
plot	boolean. Default: FALSE. Whether the heatmap should be printed or not
method	character string, name of the agglomeration method to be used (hclust) This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).
notecol	character string. Name of the colour to use for the annotation within the heatmap.
col	function to be used to define the colour palette for (gplots) heatmap.2 default: colorRampPalette(c('aliceblue','darkcyan'))
threshold	numeric. Default: 0
...	for labelling purposes

Value

a data.frame

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