Region Ranger.
region_ranger.RdReturn genes residing in defined region(s).
Usage
region_ranger(
these_regions = NULL,
qchrom = NULL,
qstart = NULL,
qend = NULL,
projection = "hg38",
raw = FALSE
)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.
- raw
Set to TRUE to return all columns. Default is FALSE.
Details
Query a region and return all genomic events residing inside the specified region. 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
region_ranger(these_regions = "chr8:127735434-127742951")
#> region_start region_end type gene_biotype hugo_symbol ensembl_gene_id chrom
#> 1 127735434 127742951 gene lncRNA CASC11 ENSG00000249375 chr8
#> 2 127735434 127742951 gene protein_coding MYC ENSG00000136997 chr8
#> start end width strand
#> 1 127686343 127738987 52645 -
#> 2 127735434 127742951 7518 +
#Example 2 - Give the function multiple regions as a string
region_ranger(these_regions = c("chr8:128747680-128753674",
"chr18:60790579-60987361"),
projection = "grch37")
#> region_start region_end type gene_biotype hugo_symbol ensembl_gene_id
#> 1 60790579 60987361 gene protein_coding BCL2 ENSG00000171791
#> 2 60790579 60987361 gene sense_intronic RP11-299P2.1 ENSG00000267766
#> 3 60790579 60987361 gene snoRNA snoU13 ENSG00000238988
#> 4 60790579 60987361 gene sense_intronic RP11-28F1.2 ENSG00000267701
#> 5 128747680 128753674 gene protein_coding MYC ENSG00000136997
#> chrom start end width strand
#> 1 18 60790579 60987361 196783 -
#> 2 18 60818347 60818553 207 -
#> 3 18 60861822 60861898 77 -
#> 4 18 60981035 60981315 281 -
#> 5 8 128747680 128753674 5995 +
#Example 3 - Individually specify the chromosome, start and end coordinates
region_ranger(qchrom = "chr8",
qstart = 127735434,
qend = 127742951)
#> region_start region_end type gene_biotype hugo_symbol ensembl_gene_id chrom
#> 1 127735434 127742951 gene lncRNA CASC11 ENSG00000249375 chr8
#> 2 127735434 127742951 gene protein_coding MYC ENSG00000136997 chr8
#> start end width strand
#> 1 127686343 127738987 52645 -
#> 2 127735434 127742951 7518 +
#Example 4 - Individually specify multiple regions with the query parameters
region_ranger(qchrom = c("chr8", "chr18"),
qstart = c(128747680, 60790579),
qend = c(128753674, 60987361),
projection = "grch37")
#> region_start region_end type gene_biotype hugo_symbol ensembl_gene_id
#> 1 60790579 60987361 gene protein_coding BCL2 ENSG00000171791
#> 2 60790579 60987361 gene sense_intronic RP11-299P2.1 ENSG00000267766
#> 3 60790579 60987361 gene snoRNA snoU13 ENSG00000238988
#> 4 60790579 60987361 gene sense_intronic RP11-28F1.2 ENSG00000267701
#> 5 128747680 128753674 gene protein_coding MYC ENSG00000136997
#> chrom start end width strand
#> 1 18 60790579 60987361 196783 -
#> 2 18 60818347 60818553 207 -
#> 3 18 60861822 60861898 77 -
#> 4 18 60981035 60981315 281 -
#> 5 8 128747680 128753674 5995 +