getCormat {Biopeak} | R Documentation |
The getCormat function calculates a pair-wise correlation matrix and plots a bi-clustered heatmap.
getCormat(peakdet, exprmat, method = "spearman")
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'). |
Returns both the heatmap object and the re-ordered correlation matrix:
David Lauenstein
# 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')