makeCNEDensity: Make 'Bed', 'bedGraph' and 'BigWig' files

In ge11232002/CNEr: CNE Detection and Visualization

Make ‘Bed’, ‘bedGraph’ and ‘BigWig’ files

Description

Make ‘Bed’, ‘bedGraph’, ‘BigWig’ files from GRangePairs for display in other Genome Browser.

Usage

  makeCNEDensity(x, outputDir = ".", 
                 genomeFirst = "first", genomeSecond = "second",
                 threshold = "50_50", 
                 windowSizeFirst = 300L, windowSizeSecond = 300L)

Arguments

x	GRangePairs object of CNEs.
outputDir	character(1): the output directory of ‘Bed’, ‘bedGraph’ and ‘BigWig’ files.
genomeFirst,genomeSecond	character(1): the genome name of the first and second species.
threshold	character(1): the threshold used to identify the CNEs in format of "50_50".
windowSizeFirst,windowSizeSecond	integer(1): the smoothing window size for generating the CNE density in kb.

Details

The CNE density is defined as the percentage of regions covered by CNEs within the smoothing window.

Value

The filenames of output ‘Bed’, ‘bedGraph’ and ‘BigWig’ files.

Note

This function is mainly for internal use in Lenhard group.

Author(s)

Ge Tan

See Also

readAncora

Examples

  ## Not run: 
  dbName <- file.path(system.file("extdata", package="CNEr"),
                      "danRer10CNE.sqlite")
  qAssemblyFn <- file.path(system.file("extdata",
                                       package="BSgenome.Hsapiens.UCSC.hg38"),
                           "single_sequences.2bit")
  tAssemblyFn <- file.path(system.file("extdata",
                             package="BSgenome.Drerio.UCSC.danRer10"),
                           "single_sequences.2bit")
  cneGRangePairs <- readCNERangesFromSQLite(dbName=dbName,
                                            tableName="danRer10_hg38_45_50",
                                            tAssemblyFn=tAssemblyFn,
                                            qAssemblyFn=qAssemblyFn)
  makeCNEDensity(cneGRangePairs[1:1000])
  
## End(Not run)

ge11232002/CNEr documentation built on Oct. 26, 2022, 7:08 p.m.