Orders a vector of indices according to their corresponding genomic locations (chromosome and position). This function is useful for sorting site sites or other genomic features by their physical positions.

Usage

orderByLoc(
  x,
  array = c("450K", "27K", "EPIC", "EPICv2"),
  genome = c("hg38", "hg19", "hs1", "mm10", "mm39"),
  genomic_locs = NULL
)

Arguments

x: Character or integer vector. Indices or identifiers to be ordered
array: Character. Array platform type, either "450K" or "EPIC" (default: "450K")
genome: Character. Genome version, either "hg38", "hg19", or "hs1" (default: "hg38")
genomic_locs: Data frame. Optional pre-computed genomic locations. If NULL, locations will be retrieved using getSortedGenomicLocs (default: NULL)

Value

Integer vector of ordered indices

Examples

# Order site indices by genomic location
site_ids <- c("cg00000029", "cg00000108", "cg00000109")
ordered_indices <- orderByLoc(site_ids, array = "450K")

# Order using pre-computed genomic locations
locs <- getSortedGenomicLocs("EPIC", "hg38")
ordered_indices <- orderByLoc(site_ids, genomic_locs = locs)