txLoc-class: 'txLoc' object.

In mevers/RNAModR: Functional Analysis of RNA Modifications

Description

The S4 object stores information about mapped loci per transcript region.

Details

The txLoc S4 object contains the following four slots:

1. loci: A list of DataFrame objects, each with the following columns:

   • locus_in_txx_region: A GRanges object

   • locus_in_genome: A GRanges object

   • score: A numeric vector

   • id: A character vector

   • tx_region: A character vector

   • tx_region_width: An integer vector

   • tx_region_sequence: A DNAStringSet object

   • tx_refseq: A character vector

   • gene_entrez: A character vector

   • gene_symbol: A character vector

   • gene_ensembl: A character vector

   • gene_name: A character vector

   The loci slot can be accessed using GetLoci(txLoc).

2. id: An identifier specified by the user. The id slot can be accessed using GetId(txLoc).

3. refGenome: The reference genome version (e.g. "hg38"), which determines the mapping between genomic and transcriptomic coordinates. The refGenome slot can be accessed using GetRef(txLoc).

4. 'version': A version identifier; currently this slot is used to to store the current system time & date. The version slot can be accessed using GetVersion(txLoc).

Slots

loci

A list of DataFrame objects; see 'Details'.

id

A character string; see 'Details.

refGenome

A character string; see 'Details'.

version

A character string; see 'Details'.

Author(s)

Maurits Evers, [e-mail]

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