R/ranges-construct.R
ranges-construct.RdThe as_i(g)ranges function looks for column names in .data called start, end, width, seqnames and strand in order to construct an IRanges or GRanges object. By default other columns in .data are placed into the mcols ( metadata columns) slot of the returned object.
as_iranges(.data, ..., keep_mcols = TRUE)
as_granges(.data, ..., keep_mcols = TRUE)a data.frame() or tibble() to
construct a Ranges object from
optional named arguments specifying which the columns in .data containin the core components a Ranges object.
place the remaining columns into the metadata columns slot (default=TRUE)
a Ranges object.
df <- data.frame(start=c(2:-1, 13:15), width=c(0:3, 2:0))
as_iranges(df)
#> IRanges object with 7 ranges and 0 metadata columns:
#> start end width
#> <integer> <integer> <integer>
#> [1] 2 1 0
#> [2] 1 1 1
#> [3] 0 1 2
#> [4] -1 1 3
#> [5] 13 14 2
#> [6] 14 14 1
#> [7] 15 14 0
df <- data.frame(start=c(2:-1, 13:15), width=c(0:3, 2:0), strand = "+")
# will return an IRanges object
as_iranges(df)
#> IRanges object with 7 ranges and 1 metadata column:
#> start end width | strand
#> <integer> <integer> <integer> | <character>
#> [1] 2 1 0 | +
#> [2] 1 1 1 | +
#> [3] 0 1 2 | +
#> [4] -1 1 3 | +
#> [5] 13 14 2 | +
#> [6] 14 14 1 | +
#> [7] 15 14 0 | +
df <- data.frame(start=c(2:-1, 13:15), width=c(0:3, 2:0),
strand = "+", seqnames = "chr1")
as_granges(df)
#> GRanges object with 7 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 2-1 +
#> [2] chr1 1 +
#> [3] chr1 0-1 +
#> [4] chr1 -1-1 +
#> [5] chr1 13-14 +
#> [6] chr1 14 +
#> [7] chr1 15-14 +
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# as_g/iranges understand alternate name specification
df <- data.frame(start=c(2:-1, 13:15), width=c(0:3, 2:0),
strand = "+", chr = "chr1")
as_granges(df, seqnames = chr)
#> GRanges object with 7 ranges and 0 metadata columns:
#> seqnames ranges strand
#> <Rle> <IRanges> <Rle>
#> [1] chr1 2-1 +
#> [2] chr1 1 +
#> [3] chr1 0-1 +
#> [4] chr1 -1-1 +
#> [5] chr1 13-14 +
#> [6] chr1 14 +
#> [7] chr1 15-14 +
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths
# can also handle DFrame input
df <- methods::as(df, "DFrame")
df$y <- IRanges::IntegerList(c(1,2,3), NA, 5, 6, 8, 9, 10:12)
as_iranges(df)
#> IRanges object with 7 ranges and 3 metadata columns:
#> start end width | strand chr y
#> <integer> <integer> <integer> | <character> <character> <IntegerList>
#> [1] 2 1 0 | + chr1 1,2,3
#> [2] 1 1 1 | + chr1 <NA>
#> [3] 0 1 2 | + chr1 5
#> [4] -1 1 3 | + chr1 6
#> [5] 13 14 2 | + chr1 8
#> [6] 14 14 1 | + chr1 9
#> [7] 15 14 0 | + chr1 10,11,12
as_granges(df, seqnames = chr)
#> GRanges object with 7 ranges and 1 metadata column:
#> seqnames ranges strand | y
#> <Rle> <IRanges> <Rle> | <IntegerList>
#> [1] chr1 2-1 + | 1,2,3
#> [2] chr1 1 + | <NA>
#> [3] chr1 0-1 + | 5
#> [4] chr1 -1-1 + | 6
#> [5] chr1 13-14 + | 8
#> [6] chr1 14 + | 9
#> [7] chr1 15-14 + | 10,11,12
#> -------
#> seqinfo: 1 sequence from an unspecified genome; no seqlengths