makeCNEDensity {CNEr} | R Documentation |
Make ‘Bed’, ‘bedGraph’, ‘BigWig’ files
from GRangePairs
for
display in other Genome Browser.
makeCNEDensity(x, outputDir = ".", genomeFirst = "first", genomeSecond = "second", threshold = "50_50", windowSizeFirst = 300L, windowSizeSecond = 300L)
x |
|
outputDir |
|
genomeFirst,genomeSecond |
|
threshold |
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windowSizeFirst,windowSizeSecond |
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The CNE density is defined as the percentage of regions covered by CNEs within the smoothing window.
The filenames of output ‘Bed’, ‘bedGraph’ and ‘BigWig’ files.
This function is mainly for internal use in Lenhard group.
Ge Tan
## 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)