as_iranges {plyranges} | R Documentation

## 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)

[Package plyranges version 1.14.0 Index]