annotation2fasta: write probes in FASTA

Description Usage Arguments Details Value Author(s) Examples

View source: R/10_1_annotation2fasta.R

Description

Fasta files from a pd.annotation object

Usage

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annotation2fasta(originalAnnotationDir, celFilePath = "InputFilePath", author,
  email, organism, species, outputDir, reverse = FALSE)

Arguments

originalAnnotationDir

directory that contains annotation files: ".pgf", ".clf", ".probeset.csv", ".mps" and ".mps" files, if annotation is PGF-based; ".cdf" – Chip Definition file, ".CEL" – example CEL file, "probe_tab" – tabulated .txt probes file

celFilePath

path to CEL file, if not present in originalAnnotationDir and annotation is CDF-based

author

character, name of the annotation package author

email

character e-mail of the annotation package author (must contain "@")

organism

character (ex: "Human")

species

character (ex: "Homo Sapiens")

outputDir

path to user-spesified output directory

reverse

logical, if reverse = TRUE, probe sequences are written in reverse order (not reverse complementary)

Details

Fasta files with pobe sequences generated from a parsed data object (probe sequences and ids from original annotation).

Value

writes "FASTA" file in directory outpurDir/Probe_Sequences_Fasta/ (created the directory if needed)

Author(s)

Vladislava Milchevskaya milchv@gmail.com

Examples

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dir1 = "/Users/milchevs/ownCloud/ProbeRemapSteps14/inst/extdata/mogene2_affyLibFiles_pgfBased/"
outDir = "/Users/milchevs/ownCloud/ProbeRemapSteps14/OutPutDir/"
dir.create(outDir)
annotation2fasta(originalAnnotationDir = dir1, 
                organism = "Mouse", species = "Mus musculus", 
                author = "Vladislava Milchevskaya",
                email = "milchv@gmail.com",
                outputDir = outDir, 
                reverse = FALSE)

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