refseq_mRNAfeat: Get mRNA features

In refseqR: Common Computational Operations Working with RefSeq Entries (GenBank)

Get mRNA features

Description

refseq_mRNAfeat() Returns a number of features from a single/multiple mRNA accession(s).

Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.

Usage

refseq_mRNAfeat(transcript , feat)

Arguments

transcript	A character string of the transcript id.
feat	A character string of the selected features. Allowed features: 'caption', 'moltype', 'sourcedb', 'updatedate', 'slen', 'organism', 'title'.

Value

A tibble of summarized results including columns:

• caption, mRNA accession

• moltype, type of molecule

• sourcedb, database (GenBank)

• updatedate, date of updated record

• slen, molecule length (in bp)

• organism

• title, sequence description

Author(s)

Jose V. Die

See Also

refseq_fromGene to obtain the transcript or protein accession from a single GeneID accession.

refseq_RNA2protein to obtain the protein accessions encoded by a set of transcript ids.

Examples

# Get several molecular features from a set of mRNA accessions
transcript = c("XM_004487701", "XM_004488493", "XM_004501904")
feat = c("caption", "moltype", "sourcedb", "slen")
refseq_mRNAfeat(transcript ,feat)

refseqR documentation built on Oct. 30, 2024, 1:06 a.m.