BuildTx: Build a custom transcriptome.

In mevers/RNAModR: Functional Analysis of RNA Modifications

Description

Build a custom, organism-specific transcriptome. See 'Details'.

Usage

BuildTx(genomeVersion = c("hg38", "hg19", "hg18", "mm10", "mm9", "mm8",
  "dm6", "dm3", "dm2", "sacCer3", "sacCer2", "sacCer1"), force = FALSE)

Arguments

genomeVersion	A character string; refers to a specific reference genome assembly version; default is "hg38".
force	A logical scalar; if TRUE force rebuild of transcriptome; this will overwrite existing data.

Details

The function builds an organism-specific transcriptome containing one transcript per unique Entrez ID; the transcript is selected from all UCSC RefSeq annotation-based isoforms as the transcript with the longest CDS, and longest upstream/downstream adjoining UTRs. Transcript segments are stored per transcript section, and written into a .RData file. For most operations, the user will run this function once, and continue with further downstream analyses. Various RNAModR routines will automatically load the transcriptome data to e.g. map sites to and from the transcriptome. Currently, RNAModR supports analyses of human, mouse, fruitfly and yeast data, based on different reference genome versions:

• Homo sapiens: hg38, hg19, hg18

• Mus musculus: mm10, mm9, mm8

• Drosophila melanogaster: dm6, dm3, dm2

• Cerevisiae saccharomyces: sacCer3, sacCer2, sacCer1

Reconstruction of existing transcriptome data can be achieved by running BuildTx with force = TRUE. Note that this will overwrite the existing RData file. Running BuildTx with sanityCheck = TRUE performs additional checks of the various transcriptome components, and is intended for debugging purposes only. It is usually safe to run with the default sanityCheck = FALSE.

Author(s)

Maurits Evers, [e-mail]

Examples

## Not run: 
# Build the human hg38-based reference transcriptome
BuildTx("hg38");

## End(Not run)

mevers/RNAModR documentation built on Nov. 17, 2019, 9:11 a.m.