computeMatrix: Read density per region
In e-myers/rnaseq: Process, Analyze and Visualize RNA-seq Data

Description Usage Arguments Details Author(s) Examples

Write matrix containing read density per region from bigwig files

computeMatrix(inFiles, regionsFiles, deeptoolsPath = "", outDest = "./",
  outSuffix = "", textMatrix = FALSE, startLabel = NULL,
  endLabel = NULL, skipZeros = FALSE, missingDataAsZero = FALSE,
  maxThreshold = NULL, minThreshold = NULL, upstream = 0,
  downstream = 0, regionBodyLength = 1000, binSize = 10,
  nProcessors = 1)

`inFiles`	Character - List of BAM files
`deeptoolsPath`	String - Path to deeptools directory
`outDest`	String - Directory where matrix files should be written
`outSuffix`	String - will be appended to original filename (and ".bedgraph" is replaced by ".bigwig")
`genomeSizeFile`	String - Filename (with path) to text file containing genome size information

Take a list of bigwigs and use the deeptools computeMatrix function to get a matrix file for each, which can then be used by plotHeatmap to create an eps. TIME: Varies a lot, maybe based on how many cores you're using? 15-35m per bigwig is typical. COMMAND LINE EXAMPLE (if you want to play with the parameters while looking at just one file, this might be easiest): computeMatrix scale-regions -S samplename.bw -R All_mm10_wholeGenes.bed -b 1000 -a 1000 –skipZeros -o samplename_regions.mat.gz -p 2 IMPROVE: Have it write the deeptools command to the top of the file where text printed to screen gets sent. Make it so you can do reference-point instead of scale-regions. Could be two different functions if the options are really different. a and b have different defaults. Don't bother making it possible to group bigwigs. They're still separate plots, just in the same output file.

Emma Myers