toGenomeOrder {genoset} | R Documentation

## Set a GRanges or GenoSet to genome order

### Description

Returns a re-ordered object sorted by chromosome and start position. If strict=TRUE, then chromosomes must be in order specified by chrOrder. If ds is already ordered, no re-ordering is done. Therefore, checking order with isGenomeOrder, is unnecessary if order will be corrected if isGenomeOrder is FALSE.

### Usage

    toGenomeOrder(ds, strict = TRUE)

### Arguments

`ds` | GenoSet or GRanges
`strict` | logical, should chromosomes be in order specified by chrOrder?

### Details

toGenomeOrder for GRanges differs from sort in that it orders by chromsome and start position only, rather than chromsome, strand, start, and width.

### Value

re-ordered ds

### See Also

Other 'genome ordering': `chrOrder`, `isGenomeOrder`

### Examples

      data(genoset,package='genoset')
      toGenomeOrder( genoset.ds, strict=TRUE )
      toGenomeOrder( genoset.ds, strict=FALSE )
      toGenomeOrder( rowRanges(genoset.ds) )

[Package genoset version 1.45.1 Index]