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

View source: R/Ancora.R

makeCNEDensityR Documentation

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.