make_objects_for_reannotation: Converts ProbeSets to package building input

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

Description

convert ProbeSets to a format needed for package building

Usage

make_objects_for_reannotation(Probesets, level = "gene", Annotation, shift)

Arguments

Probesets	data.frame, must contain columns "transcript_id", "gene_id" and "probe_id"
level	character, must be "gene" or "transcript"
Annotation	reference genome annotation data.frame
shift	numeric, a constant that is being added to all main probe set ids, in order to make them larger than control probe set ids (and thus avoid same probe set ids when unwanted)

Details

Converts ProbeSets data.frame into a list of two data.frames: ProbeSetDataAnnotation and ProbeSetDataFrame. The ProbeSetDataAnnotation contains 4 colunms: fsetname, fsetid, strand, chrom, where fsetname is an Ensembl gene/transcript ID. The ProbeSetDataFrame contains two colunms: fsetid and fid, where fid is a probe ID from the original array annotation.

Value

a list with two data.frames

Author(s)

Vladislava Milchevskaya [e-mail]

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