getCormat: Identification of co-expressing genes

In Biopeak: Identification of Impulse-Like Gene Expression Changes in Short Genomic Series Data

Description

The getCormat function calculates a pair-wise correlation matrix and plots a bi-clustered heatmap.

Usage

getCormat(peakdet, exprmat, method = "spearman")

Arguments

peakdet	A list returned by the peakDetection function.
exprmat	A numeric matrix with expression series data with variables as rownames.
method	A character string defining the correlation algorithm. Options are: c('pearson', 'kendall', 'spearman').

Value

Returns both the heatmap object and the re-ordered correlation matrix:

Author(s)

David Lauenstein

Examples

# Example based on the heat-shock dataset
data(heat)
heat = as.matrix(heat)
# Define series
series <- c(37,40,41,42,43)
# Run the peak detection algorithm
peakdet <- peakDetection(heat, series, type ='rnaseq', actstrength = 1.5,
prominence = 1.3, minexpr = 5000)
# calculate and plot correlation matrix
corobjects <- getCormat(peakdet, heat, method = 'spearman')

Biopeak documentation built on Aug. 21, 2019, 5:10 p.m.