assignFirstExonsStartSite {ORFik} | R Documentation

## Reassign the start positions of the first exons per group in grl

### Description

Per group in GRangesList, assign the most upstream site.

### Usage

    assignFirstExonsStartSite(
      grl,
      newStarts,
      is.circular = all(isCircular(grl) %in% TRUE)
    )

### Arguments

`grl` | a `GRangesList` object
`newStarts` | an integer vector of same length as grl, with new start values (absolute coordinates, not relative)
`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.

### Details

make sure your grl is sorted, since start of "-" strand objects should be the max end in group, use ORFik:::sortPerGroup(grl) to get sorted grl.

### Value

the same GRangesList with new start sites

### See Also

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

[Package ORFik version 1.12.13 Index]