BPCells fragments can be interconverted with GRanges and data.frame R objects.
The main conversion method is R's builtin as() function, though the
convert_to_fragments() helper is also available. For all R objects except
GRanges, BPCells assumes a 0-based, end-exclusive coordinate system. (See
genomic-ranges-like reference for details)
Usage
# Convert from R to BPCells
convert_to_fragments(x, zero_based_coords = !is(x, "GRanges"))
as(x, "IterableFragments")
# Convert from BPCells to R
as.data.frame(bpcells_fragments)
as(bpcells_fragments, "data.frame")
as(bpcells_fragments, "GRanges")Arguments
- x
Fragment coordinates given as GRanges, data.frame, or list. See
help("genomic-ranges-like")for details on format and coordinate systems. Required attributes:chr,start,end: genomic positioncell_id: cell barcodes or unique identifiers as string or factor
- zero_based_coords
Whether to convert the ranges from a 1-based end-inclusive coordinate system to a 0-based end-exclusive coordinate system. Defaults to true for GRanges and false for other formats (see this archived UCSC blogpost)
Examples
frags_table <- tibble::tibble(
chr = paste0("chr", 1:10),
start = 0,
end = 5,
cell_id = "cell1"
)
frags_table
#> # A tibble: 10 × 4
#> chr start end cell_id
#> <chr> <dbl> <dbl> <chr>
#> 1 chr1 0 5 cell1
#> 2 chr2 0 5 cell1
#> 3 chr3 0 5 cell1
#> 4 chr4 0 5 cell1
#> 5 chr5 0 5 cell1
#> 6 chr6 0 5 cell1
#> 7 chr7 0 5 cell1
#> 8 chr8 0 5 cell1
#> 9 chr9 0 5 cell1
#> 10 chr10 0 5 cell1
frags_granges <- GenomicRanges::makeGRangesFromDataFrame(
frags_table, keep.extra.columns = TRUE
)
frags_granges
#> GRanges object with 10 ranges and 1 metadata column:
#> seqnames ranges strand | cell_id
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chr1 0-5 * | cell1
#> [2] chr2 0-5 * | cell1
#> [3] chr3 0-5 * | cell1
#> [4] chr4 0-5 * | cell1
#> [5] chr5 0-5 * | cell1
#> [6] chr6 0-5 * | cell1
#> [7] chr7 0-5 * | cell1
#> [8] chr8 0-5 * | cell1
#> [9] chr9 0-5 * | cell1
#> [10] chr10 0-5 * | cell1
#> -------
#> seqinfo: 10 sequences from an unspecified genome; no seqlengths
#######################################################################
## convert_to_fragments() example
#######################################################################
frags <- convert_to_fragments(frags_granges)
frags
#> IterableFragments object of class "UnpackedMemFragments"
#>
#> Cells: 1 cells with names cell1
#> Chromosomes: 10 chromosomes with names chr1, chr2 ... chr10
#>
#> Queued Operations:
#> 1. Read uncompressed fragments from memory
#######################################################################
## as(x, "IterableFragments") example
#######################################################################
frags <- as(frags_table, "IterableFragments")
frags
#> IterableFragments object of class "UnpackedMemFragments"
#>
#> Cells: 1 cells with names cell1
#> Chromosomes: 10 chromosomes with names chr1, chr10 ... chr9
#>
#> Queued Operations:
#> 1. Read uncompressed fragments from memory
#######################################################################
## as(bpcells_fragments, "data.frame") example
#######################################################################
frags_table <- as(frags, "data.frame")
frags_table
#> chr start end cell_id
#> 1 chr1 0 5 cell1
#> 2 chr10 0 5 cell1
#> 3 chr2 0 5 cell1
#> 4 chr3 0 5 cell1
#> 5 chr4 0 5 cell1
#> 6 chr5 0 5 cell1
#> 7 chr6 0 5 cell1
#> 8 chr7 0 5 cell1
#> 9 chr8 0 5 cell1
#> 10 chr9 0 5 cell1
#######################################################################
## as(bpcells_fragments, "GRanges") example
#######################################################################
frags_granges <- as(frags, "GRanges")
frags_granges
#> GRanges object with 10 ranges and 1 metadata column:
#> seqnames ranges strand | cell_id
#> <Rle> <IRanges> <Rle> | <factor>
#> [1] chr1 1-5 * | cell1
#> [2] chr10 1-5 * | cell1
#> [3] chr2 1-5 * | cell1
#> [4] chr3 1-5 * | cell1
#> [5] chr4 1-5 * | cell1
#> [6] chr5 1-5 * | cell1
#> [7] chr6 1-5 * | cell1
#> [8] chr7 1-5 * | cell1
#> [9] chr8 1-5 * | cell1
#> [10] chr9 1-5 * | cell1
#> -------
#> seqinfo: 10 sequences from an unspecified genome; no seqlengths
