ranges-construct: Construct a I/GRanges object from a tibble or data.frame

In sa-lee/plyranges: A fluent interface for manipulating GenomicRanges

Construct a I/GRanges object from a tibble or data.frame

Description

The 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.

Usage

as_iranges(.data, ..., keep_mcols = TRUE)

as_granges(.data, ..., keep_mcols = TRUE)

Arguments

.data	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.
keep_mcols	place the remaining columns into the metadata columns slot (default=TRUE)

Value

a Ranges object.

See Also

IRanges::IRanges(), GenomicRanges::GRanges()

Examples

df <- data.frame(start=c(2:-1, 13:15), width=c(0:3, 2:0))
as_iranges(df)

df <- data.frame(start=c(2:-1, 13:15), width=c(0:3, 2:0), strand = "+")
# will return an IRanges object
as_iranges(df)

df <- data.frame(start=c(2:-1, 13:15), width=c(0:3, 2:0),
strand = "+", seqnames = "chr1")
as_granges(df)

# 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)

# 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)
as_granges(df, seqnames = chr)

sa-lee/plyranges documentation built on April 15, 2024, 12:25 p.m.