calcSplineMItoFile: Calculates MI matrix and write directly to file

In larsgr/BSplineMI: Mutual information using B-Spline smoothed bins

Description

Calculates specified rows of lower half of MI matrix and write directly to file. This uses less memory as it doesn't need to hold the entire mi matrix in memory. By setting fromRow and toRow it is possible to split up the job to run independantly in parallel.

Usage

calcSplineMItoFile(x, nBins, splineOrder, filename, fromRow = 2,
  toRow = nrow(x))

Arguments

x	Gene expression matrix with genes in rows and samples in columns
nBins	Number of bins
splineOrder	Spline order
filename	name of output file
fromRow	first row of MI matrix to generate
toRow	last row of MI matrix to generate

Value

Returns nothing. The results are written to file as text with values space separated and one row per line. Gene IDs are discarded.

Examples

tmp <- tempfile()
data(riceEx)
calcSplineMItoFile( riceEx, 7, 3, filename = tmp, fromRow = 4, toRow = 6 )
cat(readLines(tmp),sep="\n")
unlink(tmp)

larsgr/BSplineMI documentation built on May 20, 2019, 7:57 p.m.