toGenomeOrder: Set a GRanges or GenoSet to genome order

In genoset: A RangedSummarizedExperiment with methods for copy number analysis

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) )

genoset documentation built on Nov. 8, 2020, 6:07 p.m.