Skip to contents

Get sequence of genomic target regions

Source: R/get_seq.R
get_seq.Rd

Create a GRanges object from the genomic target ranges and import raw nucleotide sequences.

Usage

get_seq(
  regions,
  rg_sep = "\t",
  is_0_based_rg = TRUE,
  padding = 0,
  BS_genome = NULL,
  ucsc = FALSE,
  species = NULL,
  genome = NULL
)

Arguments

regions

The regions metadata file to import. Can be either a file path, a data frame, or a GRanges object. File paths will be read using the rg_sep. Users can also choose from the built-in TwinStrand's Mutagenesis Panels by inputting "TSpanel_human", "TSpanel_mouse", or "TSpanel_rat". Required columns for the regions file are "contig", "start", and "end". In a GRanges object, the required columns are "seqnames", "start", and "end".

rg_sep

The delimiter for importing the regions file. The default is tab-delimited ("\t").

is_0_based_rg

A logical variable. Indicates whether the position coordinates in regions are 0 based (TRUE) or 1 based (FALSE). If TRUE, positions will be converted to 1-based (start + 1). Need not be supplied for TSpanels. Default is TRUE.

padding

An integer value by which the function will extend the range of the target sequence on both sides. Start and end coordinates will be adjusted accordingly. Default is 0.

BS_genome

The name of the appropriate BSgenome package to use for sequence retrieval. Ex. "BSgenome.Hsapiens.UCSC.hg38", "BSgenome.Mmusculus.UCSC.mm10", "BSgenome.Rnorvegicus.UCSC.rn6". Use the function find_BS_genome() to help identify the appropriate BSgenome package if needed. Need not be supplied for TSpanels. BS_genome must be installed if using this method.

ucsc

A logical value. If TRUE, the function will retrieve the sequences from the UCSC genome browser using an API. If FALSE, the function will retrieve sequences using the appropriate BSgenome package, which will be installed as needed. Default is FALSE.

species

The species for which to retrieve the sequences. Only required if using the UCSC method. Species may be given as the scientific name or the common name. Ex. "Human", "Homo sapien". Used to choose the appropriate BS genome. Need not be supplied for TSpanels.

genome

The genome assembly version for which to retrieve the sequences. Only required if using the UCSC method. Ex. hg38, hg19, mm10, mm39, rn6, rn7. Need not be supplied for TSpanels.

Value

a GRanges object with sequences of targeted regions.

Details

Consult available.genomes(splitNameParts=FALSE, type=getOption("pkgType")) for a full list of the available BS genomes and their associated species/genome/masked values. The BSgenome package will be installed if not already available. If using the UCSC API, the function will retrieve the sequences from the UCSC genome browser using the DAS API. See the UCSC website for available genomes: https://genome.ucsc.edu.

Examples

# Example 1: Retrieve the sequences for TwinStrand Mouse Mutagenesis Panel
regions_seq <- get_seq(regions = "TSpanel_mouse")
#> Loading reference genome: BSgenome.Mmusculus.UCSC.mm10.
#> 
#> Attaching package: ‘generics’
#> The following objects are masked from ‘package:base’:
#> 
#>     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#>     setequal, union
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#>     unsplit, which.max, which.min
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> 
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:base’:
#> 
#>     strsplit

# Example 2: Retrieve the sequences for custom regions
# We will load the TSpanel_human regions file as an example
# and supply it to the function as a GRanges object.
human <- load_regions_file("TSpanel_human")
regions_seq <- get_seq(
  regions = human,
  is_0_based_rg = FALSE,
  BS_genome = "BSgenome.Hsapiens.UCSC.hg38",
  padding = 0
)
#> Loading reference genome: BSgenome.Hsapiens.UCSC.hg38.