annotateGetRefFromTranscriptDb: Get mapping between reference and gene using TranscriptDb

In ProbeAnnotator: Faste Gene Annotation in R

Description

Gets the mapping between reference (usually transcripts) and gene's EntrezID using a TranscriptDb object.

Usage

annotateGetRefFromTranscriptDb(txDb, exons, verbose = FALSE)

Arguments

txDb	A TranscriptDb object.
exons	A logical value, indicating if exons should be extracted.
verbose	A logical value, indicating if messages should be printed. Default is FALSE.

Value

• df_GENETR A data.frame containing the genomic ranges of the transcripts, ordered by chromosome and strand;

• df_EXON A data.frame containing the genomic ranges of the exons, ordered by chromosome and strand.

• stack_EXON A data.frame containing mappings between exons in df_EXON and transcripts in df_GENETR.

• txDb_Key A character vector, giving the EntrezID's column name.

• txGroup A data.frame containing the index of each chromosome and strand pair df_GENETR. Used to speed up computation

Author(s)

Alexandre Thiery

ProbeAnnotator documentation built on May 2, 2019, 5:49 p.m.