upstreamOfPerGroup {ORFik} | R Documentation

## Get rest of objects upstream (exclusive)

### Description

Per group get the part upstream of position upstreamOfPerGroup(tx, startSites(cds, asGR = TRUE)) will return the 5' utrs per transcript, usually used for interesting parts of the transcripts.

### Usage

    upstreamOfPerGroup(
      tx,
      upstreamOf,
      allowOutside = TRUE,
      is.circular = all(isCircular(tx) %in% TRUE)
    )

### Arguments

`tx` | a `GRangesList`, usually of Transcripts to be changed
`upstreamOf` | a vector of integers, for each group in tx, where is the the base after the new stop point of last valid exon.
`allowOutside` | a logical (T), can upstreamOf extend outside range of tx, can set boundary as a false hit, so beware.
`is.circular` | logical, default FALSE if not any is: all(isCircular(grl) Where grl is the ranges checked. If TRUE, allow ranges to extend below position 1 on chromosome. Since circular genomes can have negative coordinates.

### Value

a GRangesList of upstream part

### See Also

Other GRanges: `assignFirstExonsStartSite()`, `assignLastExonsStopSite()`, `downstreamFromPerGroup()`, `downstreamOfPerGroup()`, `upstreamFromPerGroup()`

[Package ORFik version 1.12.13 Index]