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Make linked transcript data (linked GRanges)

Source: R/linkedTxome.R
linkedTxpData.Rd

linkedTxpData allows the user to save relevant GRanges transcript data for identifying and updating transcript metadata in a persistent manner across R sessions. It can be used in combination with inspectDigests() and updateMetadata(). This is a lightweight version of linkedTxome (see makeLinkedTxome()), which requires specifying a GTF file for building a TxDb and optionally a FASTA file for sequence retrieval.)

Usage

makeLinkedTxpData(
  digest,
  digestType = "sha256",
  indexName,
  txpData,
  source,
  organism,
  release,
  genome
)

Arguments

digest

character string of the full digest of the reference transcripts, see inspectDigests() with fullDigest=TRUE

digestType

character string of the digest, default "sha256"

indexName

a name for the index when storing the linkedTxpData,

txpData

GRanges providing information about ranges representing the transcript sequences linked to digest

source

the source of transcriptome, e.g. denovo. See makeLinkedTxome() for more information on specifying source

organism

organism (e.g. "Homo sapiens")

release

release number (e.g. "27")

genome

genome (e.g. "GRCh38", or "none")

Value

nothing, the function is run for its side effects

Details

The txpData object is saved in the getTximetaBFC() location, appended with a 32-character substring of digest. The tibble listing all linkedTxpData is named linkedTxpDataTbl and is listed in the same location.

Examples


novel <- data.frame(seqnames = paste0("chr", rep(1:22, each=500)),
  start = 1e6 + 1 + 0:499 * 1000, end = 1e6 + 1 + 0:499 * 1000 + 1000 - 1,
  strand = "+", tx_name = paste0("novel", 1:(22*500)), 
  gene_id = paste0("novel_gene", rep(1:(22*10), each=50)), 
type = "protein_coding")
novel_gr <- as(novel, "GRanges")
names(novel_gr) <- novel$tx_name

makeLinkedTxpData(
 digest = "43158f2c8e88e3acd77c22aee557625a6f1b6a5038cfc7deb5e64903892d8070",
 digestType = "sha256",
 indexName = "my_novel_txps",
 txpData = novel_gr,
 source = "novel", organism="Homo sapiens", 
 release="v1", genome="GRCh38"
)
#> linking user-provided metadata to digest: 43158f...
#> saving txpData object in bfc
#> saving linkedTxpData in bfc (first time)

# to clear the entire linkedTxome table
# (don't run unless you want to clear this table!)
# bfcloc <- getTximetaBFC()
# bfc <- BiocFileCache(bfcloc)
# bfcremove(bfc, bfcquery(bfc, "linkedTxpDataTbl")$rid)