A helper function to import the regions metadata file and return a GRanges object.
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 custom_regions. The default is tab-delimited "\t".
- is_0_based_rg
A logical variable. Indicates whether the position coordinates in
regionsare 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.
Examples
#' # Example 1: Load built-in TwinStrand's Human Mutagenesis
human_rg <- load_regions_file(regions = "TSpanel_human")
human_rg
#> GRanges object with 20 ranges and 6 metadata columns:
#> seqnames ranges strand | target_size description
#> <Rle> <IRanges> <Rle> | <integer> <character>
#> [1] chr11 108510788-108513187 * | 2400 region_1111
#> [2] chr13 75803913-75806312 * | 2400 region_1501
#> [3] chr14 74661756-74664155 * | 2400 region_1725
#> [4] chr18 5749265-5751664 * | 2400 region_2457
#> [5] chr2 40162768-40165167 * | 2400 region_2896
#> ... ... ... ... . ... ...
#> [16] chr15 46089738-46092137 * | 2400 region_1904
#> [17] chr17 70672727-70675126 * | 2400 region_2378
#> [18] chr21 23665977-23668376 * | 2400 region_3515
#> [19] chr22 48262371-48264770 * | 2400 region_3703
#> [20] chr10 128969038-128971437 * | 2400 region_784
#> genic_context gene genome label
#> <character> <character> <character> <character>
#> [1] genic EXPH5 hg38 chr11
#> [2] genic LMO7 hg38 chr13
#> [3] genic AREL1 hg38 chr14
#> [4] genic MIR3976HG hg38 chr18
#> [5] genic SLC8A1-AS1 hg38 chr2
#> ... ... ... ... ...
#> [16] intergenic <NA> hg38 chr15
#> [17] intergenic <NA> hg38 chr17
#> [18] intergenic <NA> hg38 chr21
#> [19] intergenic <NA> hg38 chr22
#> [20] intergenic <NA> hg38 chr10
#> -------
#> seqinfo: 20 sequences from an unspecified genome; no seqlengths
# Load a custom regions file from an interval list
# We will use the human TSpanel system file for this example,
# but any file can be imported.
file <- system.file("extdata",
"inputs",
"metadata",
"human_mutagenesis_panel_hg38.txt",
package = "MutSeqR"
)
custom_rg <- load_regions_file(regions = file, rg_sep = "\t", is_0_based_rg = TRUE)
custom_rg
#> GRanges object with 20 ranges and 6 metadata columns:
#> seqnames ranges strand | target_size description
#> <Rle> <IRanges> <Rle> | <integer> <character>
#> [1] chr11 108510788-108513187 * | 2400 region_1111
#> [2] chr13 75803913-75806312 * | 2400 region_1501
#> [3] chr14 74661756-74664155 * | 2400 region_1725
#> [4] chr18 5749265-5751664 * | 2400 region_2457
#> [5] chr2 40162768-40165167 * | 2400 region_2896
#> ... ... ... ... . ... ...
#> [16] chr15 46089738-46092137 * | 2400 region_1904
#> [17] chr17 70672727-70675126 * | 2400 region_2378
#> [18] chr21 23665977-23668376 * | 2400 region_3515
#> [19] chr22 48262371-48264770 * | 2400 region_3703
#> [20] chr10 128969038-128971437 * | 2400 region_784
#> genic_context gene genome label
#> <character> <character> <character> <character>
#> [1] genic EXPH5 hg38 chr11
#> [2] genic LMO7 hg38 chr13
#> [3] genic AREL1 hg38 chr14
#> [4] genic MIR3976HG hg38 chr18
#> [5] genic SLC8A1-AS1 hg38 chr2
#> ... ... ... ... ...
#> [16] intergenic <NA> hg38 chr15
#> [17] intergenic <NA> hg38 chr17
#> [18] intergenic <NA> hg38 chr21
#> [19] intergenic <NA> hg38 chr22
#> [20] intergenic <NA> hg38 chr10
#> -------
#> seqinfo: 20 sequences from an unspecified genome; no seqlengths