genoset (version 1.28.2)

isGenomeOrder: Check if a GRanges orGenoSet is in genome order

Description

Checks that rows in each chr are ordered by start. If strict=TRUE, then chromosomes must be in order specified by chrOrder. isGenomeOrder for GRanges differs from order in that it orders by chromsome and start position only, rather than chromsome, strand, start, and width.

Usage

isGenomeOrder(ds, strict = TRUE)
## S3 method for class 'GenoSet':
isGenomeOrder(ds, strict = TRUE)
## S3 method for class 'GRanges':
isGenomeOrder(ds, strict = TRUE)

Arguments

ds

GenoSet or GRanges

strict

logical, should space/chromosome order be identical to that from chrOrder?

Value

• logical

See Also

Other "genome ordering": chrOrder, toGenomeOrder

Examples

data(genoset,package="genoset")
  isGenomeOrder( rowRanges(genoset.ds) )