calcHeatmapSimilarity: Calculates the similarity between two gene expression data.

In TheJacksonLaboratory/sRACIPE_dev: Systems biology tool to simulate gene regulatory circuits

Description

Comparison is done across columns, i.e., how similar are the columns in the two dataset. For gene expression data, format data so that gene names are in rows and samples in columns.

Usage

calcHeatmapSimilarity(data.reference, data.simulation,
  cluster.cut = NULL, n.clusters = 3, p.value = 0.05, permuted.var,
  permutations = 1000, cor.method = "spearman",
  cluster.method = "ward.D2", method = "pvalue", buffer = 1e-04,
  permutation.method = "simulation", return.data = FALSE)

Arguments

data.reference	Matrix. The reference data matrix, for example, the experimental gene expression values
data.simulation	Matrix. The data matrix to be compared.
cluster.cut	(optional) Integer vector. Clsuter numbers assigned to reference data. If cluster.cut is missing, hierarchical clustering using /codeward.D2 and /codedistance = (1-cor(x, method = "spear"))/2 will be used to cluster the reference data.
n.clusters	(optional) Integer. The number of clusters in which the reference data should be clustered for comparison. Not needed if cluster.cut is provided.
p.value	(optional) Numeric. p-value to consider two gene expression sets as belonging to same cluster. Ward's method with spearman correlation is used to determine if a model belongs to a specific cluster.
permuted.var	(optional) Similarity scores computed after permutations.
cor.method	(optional) Correlation method. Default method is "spearman". For single cell data, use "kendall"
cluster.method	(optional) Character - default ward.D2, other options include complete. Clustering method to be used to cluster the experimental data. hclust for other options.
permutation.method	"sample" or "reference"

Value

A list containing the KL distance of new cluster distribution from reference data and the probability of each cluster in the reference and simulated data.

Related Functions

simulateGRC, knockdownAnalysis, overExprAnalysis, plotData, calcHeatmapSimilarity

TheJacksonLaboratory/sRACIPE_dev documentation built on May 7, 2019, 8:16 a.m.