CollapseTxBySec: Collapse entries from a 'GetTxBySec' return object.
In mevers/RNAModR: Functional Analysis of RNA Modifications

Collapse entries from a GetTxBySec return object. See 'Details'. This is a low-level function that is being called from BuildTx.

1	CollapseTxBySec(txBySec, geneXID, verbose = FALSE)

`txBySec`	A `list` of `GRangesList` objects; output of function `GetTxBySec`.
`geneXID`	A `data.frame`; output of function `GetGeneIds` providing gene IDs from different gene annotations.
`verbose`	A logical scalar; if `TRUE` print additional output; default it `FALSE`

Entries are collapsed using the following method:

If multiple entries exist for one Entrez ID, the transcript with the longest CDS is kept.
For every CDS with a unique RefSeq ID, the 5'/3'UTRs closest to the CDS (non-overlapping) is kept; in the case of a distance tie, the longest UTR is kept.
For every 5'UTR with a unique RefSeq ID, the corresponding upstream promoter is chosen.

A list of GRangesList objects

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