GetTxBySec: Get transcript sections.
In mevers/RNAModR: Functional Analysis of RNA Modifications

Description Usage Arguments Details Value Author(s)

Get transcript sections. See 'Details'. This is a low-level function that is being called from BuildTx.

1 2	GetTxBySec(txdb, sections = c("Promoter", "5'UTR", "CDS", "3'UTR"), promUpstream = 1000, promDownstream = 0, verbose = FALSE)

`txdb`	A `TxDb` object.
`sections`	A character vector; specifies which transcript sections should be extracted from `txdb`; default is `c("Promoter", "5'UTR", "CDS", "3'UTR")`.
`promUpstream`	An integer; specifies the number of nucleotides to be included upstream of 5'UTR start as part of the promoter.
`promDownstream`	An integer; specifies the number of nucleotides to be included downstream of 5'UTR start as part of the promoter.
`verbose`	A logical scalar; if `TRUE`, print additional information; default is `FALSE`

The function returns a list of GRangesList objects. The number and names of list entries match the number and names of sections. Entries in every GRangesList are labelled according to their transcript RefSeq ID. Note that multiple entries with identical RefSeq ID exist.

A list of GRangesList objects

Maurits Evers, maurits.evers@anu.edu.au

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