makeNewAnnotationPackage: What function does (short)

In VladaMilch/pdProbeRemap: What the package does (short line)

Description

Short description string here

Usage

makeNewAnnotationPackage(alignment.dir, Annotation, outputDir, level,
  min_probe_number, quiet = FALSE, pkgNameSUFFIX, fastaDir)

Arguments

alignment.dir	path to the directory that contains alignment files
Annotation	regerence genome annotation data.frame
outputDir	output directory
level	character string, can take values "gene" or "transcript", specifying if new probe sets should be formed per gene or per transcript
min_probe_number	numeric, minimal number or probes in a probe set
quiet	logical
pkgNameSUFFIX	character, suffix to the package name, usually starts with dor: '.hereIsYourSuffix'

Details

Long description string

Value

a "output type".

Author(s)

Vladislava Milchevskaya [e-mail]

See Also

function or class name

Examples

data("Alignments_class_example")
data("Annotation_example")
data("seed_example")
alignmentDir <- 
  unlist(strsplit(dir(system.file("extdata",package="pdProbeRemap"), 
                      pattern="example_drosophila.Aligned.out.sam",
                      full.names=TRUE), split = "example_drosophila.Aligned.out.sam"))[1]

outputDir_example = system.file("data", package = "pdProbeRemap")

## Not run: 
makeNewAnnotationPackage(alignment.dir = alignmentDir, 
                         Annotation = Annotation_example, 
                         outputDir = outputDir_example, 
                         level = "gene", 
                         min_probe_number = 1, 
                         pkgNameSUFFIX = ".example")
                         
## End(Not run)

VladaMilch/pdProbeRemap documentation built on May 28, 2019, 3:21 p.m.