Cyto Ranger. — cyto_ranger • biomaesteR

This function takes a region or regions and returns the cytoband information for the region(s).

Usage

cyto_ranger(
  these_regions = NULL,
  qchrom = NULL,
  qstart = NULL,
  qend = NULL,
  projection = "hg38"
)

Arguments

these_regions: The region(s) to be queried. Can be a data frame with regions with the following columns; chrom, start, end. Or in a string in the following format chr:start-end.
qchrom: Query chromosome (prefixed or un-prefixed), Required if `these_regions` is not provided.
qstart: Query start position. Required if `these_regions` is not provided.
qend: Query end position. Required if `these_regions` is not provided.
projection: The desired projection you want back coordinates for. Available projections are hg38 and grch37. Default is hg38.

Value

A data frame with cytoband information for the specified region(s).

Details

Query a region and relevant cytoband information for the specified region(s). This function accepts a variety of incoming regions. Either, regions can be provided as a data frame with `these_regions`. If so, the following columns must exist; chrom, start, end. This parameter (`these_regions`) also accept a region in "region" format, (i.e chr:start-end). This can be a region or a vector of characters with multiple regions. The user can also individually specify region(s) with; `qchrom` (string), `qstart` (string, or integer), and `qend` (string or integer). These parameters can also accept a vector of characters for multiple regions. The function also handles chromosome prefixes in the returned object, based on the selected `projection`.

Examples

#' #Example 1 - Give the function one region as a string
cyto_ranger(these_regions = "chr8:127735434-127742951")
#>   chrom region_start region_end cytoBand cytoband_start cytoband_end
#> 1  chr8    127735434  127742951   q24.21      126300000    130400000

#Example 2 - Give the function multiple regions as a string
cyto_ranger(these_regions = c("chr8:128747680-128753674",
                              "chr18:60790579-60987361"),
            projection = "grch37")
#>   chrom region_start region_end cytoBand cytoband_start cytoband_end
#> 1    18     60790579   60987361   q21.33       59000000     61600000
#> 2     8    128747680  128753674   q24.21      127300000    131500000

#Example 3 - Individually specify the chromosome, start and end coordinates
cyto_ranger(qchrom = "chr8",
            qstart = 127735434,
            qend = 127742951)
#>   chrom region_start region_end cytoBand cytoband_start cytoband_end
#> 1  chr8    127735434  127742951   q24.21      126300000    130400000

#Example 4 - Individually specify multiple regions with the query parameters
cyto_ranger(qchrom = c("chr8", "chr18"),
            qstart = c(128747680, 60790579),
            qend = c(128753674, 60987361),
            projection = "grch37")
#>   chrom region_start region_end cytoBand cytoband_start cytoband_end
#> 1    18     60790579   60987361   q21.33       59000000     61600000
#> 2     8    128747680  128753674   q24.21      127300000    131500000