get_transcripts: Get transcripts

In bschilder/echoplot: echoverse module: Locus plot creation for fine-mapping and colocalization studies

Get transcripts

Description

Get transcript positions for all genes in a range.

Usage

get_transcripts(
  gr.snp,
  max_transcripts = 1,
  remove_pseudogenes = TRUE,
  tx_biotypes = NULL,
  verbose = TRUE
)

Arguments

max_transcripts	Maximum number of transcripts per gene.
tx_biotypes	Transcript biotypes to include in the gene model track. By default (NULL), all transcript biotypes will be included. See get_tx_biotypes for a full list of all available biotypes
verbose	Print messages.

Source

#### Alternative approaches I've tried #### dat <- echodata::LRRK2 gr.snp <- echodata::dt_to_granges(dat = dat) # Warning:: MUST load the full package bc # it loads other necessary packages into the namespace. BiocManager::install("Homo.sapiens") library(Homo.sapiens) txdb <- Homo.sapiens::Homo.sapiens GenomicFeatures::genes(txdb) BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene") library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene GenomicFeatures::genes(txdb)

bschilder/echoplot documentation built on Oct. 26, 2023, 6:55 p.m.