createCorrelationMatrix: Create correlation matrix

In GabrielHoffman/decorate: Differential Epigenetic Coregulation Test

Create correlation matrix

Description

Create correlation matrix based on correlation between pairs of peaks

Usage

createCorrelationMatrix(
  query,
  regionQuant,
  adjacentCount = 500,
  windowSize = 1e+06,
  method = "adjacent",
  method.corr = c("pearson", "spearman"),
  quiet = FALSE,
  setNANtoZero = FALSE
)

Arguments

query	GRanges object of intervals to query
regionQuant	normalized quantifications of regions in query. Rows are features, like in limma
adjacentCount	number of adjacent entries to compute correlation against
windowSize	width of window in bp around each interval beyond which weight is zero
method	'adjacent': compute corr on fixed count sliding window define by adjacentCount. "distance": compute corr for entries within windowSize bp
method.corr	specify which correlation method: "pearson" or "spearman"
quiet	suppress messages
setNANtoZero	replace NAN correlation values with a zero

Value

for peak i and j with distance d_i,j, M[i,j] = cor( vobj$E[i,], vobj$E[j,] )

return sparse symmatric matrix

Examples

data('decorateData')

C = createCorrelationMatrix(simLocation, simData)

GabrielHoffman/decorate documentation built on May 23, 2023, 1:29 a.m.