write.bedGraph

Boolean.  Create a file for the raw data?

Boolean.  Create a file for the calculated p-values?

vals

directory


  Generate bedGraph format files for the UCSC genome browser.  This function will
  write the bedGraph files associated with a aGFFcalc object.  There will be
  either one or two files (default two) representing the raw data and
  the calculated data (which is output as -log10(val) for visualization
  purposes for EACH sample).  


ACME (Algorithms for Calculating Microarray Enrichment) is
a set of tools for analysing tiling array ChIP/chip, DNAse
hypersensitivity, or other experiments that result in regions
of the genome showing "enrichment".  It does not rely on a
specific array technology (although the array should be a
"tiling" array), is very general (can be applied in experiments
resulting in regions of enrichment), and is very insensitive to
array noise or normalization methods.  It is also very fast and
can be applied on whole-genome tiling array experiments quite
easily with enough memory.

Sean Davis

ACME

Algorithms for Calculating Microarray Enrichment (ACME)

write.bedGraph function

Generate bedGraph format files for the UCSC genome browser.  This function will
  write the bedGraph files associated with a aGFFcalc object.  There will be
  either one or two files (default two) representing the raw data and
  the calculated data (which is output as -log10(val) for visualization
  purposes for EACH sample).

write.bedGraph: Write bedGraph format tracks for UCSC genome browser

Description

Usage

Arguments

Examples