convert_transcriptID: Convert transcript IDs between different databases

In ShihChingYu/MRAT: Transcript Annotation Tool (TransAT): an R package for retrieving annotations for transcript specific genetic variants

Description

Preprocessing, converting and mapping

Usage

convert_transcriptID(
  dat,
  db,
  biomart_ens = "ensembl",
  dat_ens = "hsapiens_gene_ensembl",
  dat_filter = "refseq_mrna",
  BM_att_ens = c("refseq_mrna", "ensembl_transcript_id", "hgnc_symbol", "ucsc")
)

Arguments

dat	a dataframe including Transcript_version, nucleotide "C1768G" refers to ref/CDS position/alt.
db	'EnsDb' object. Default is EnsDb.Hsapiens.v75.
biomart_ens	selection of BioMart database. Default is "ensembl".
dat_ens	BioMart databases includes many datasets. Choose dataset in the database. Default is "hsapiens_gene_ensembl". Alternatives include "drerio_gene_ensembl" and "mmusculus_gene_ensembl".
dat_filter	refers to the types of transcripts. Default is "refseq_mrna". The user can also specify "ucsc" as transcript ID.
BM_att_ens	defines the values of interests. Default shows "refseq_mrna", "ensembl_transcript_id", "hgnc_symbol", "ucsc". The listAttributes function displays all available attributes in the selected dataset.

Value

a new dataset with converting information

Examples

library(EnsDb.Hsapiens.v75)
db=EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75
dat<-read.csv(system.file("extdata",
                          "convertID_refseq_data.csv",
                          package = "TransAT"),
              stringsAsFactors = FALSE, encoding = "UTF-8", row.names = NULL, sep = ",")
new_dat<-convert_transcriptID(dat, db, dat_filter = "refseq_mrna")

ShihChingYu/MRAT documentation built on May 31, 2021, 12:58 p.m.