makeGRangesListFromDataFrame {GenomicRanges} | R Documentation

## Make a GRangesList object from a data.frame or DataFrame

### Description

`makeGRangesListFromDataFrame` extends the makeGRangesFromDataFrame functionality from `GenomicRanges`. It can take a data-frame-like object as input and tries to automatically find the columns that describe the genomic ranges. It returns a GRangesList object. This is different from the `makeGRangesFromDataFrame` function by requiring a `split.field`. The `split.field` acts like the "f" argument in the `split` function. This factor must be of the same length as the number of rows in the `DataFrame` argument. The `split.field` may also be a character vector.

### Usage

    makeGRangesListFromDataFrame(df,
                                 split.field = NULL,
                                 names.field = NULL,
                                 ...)

### Arguments

`df` | A `DataFrame` or `data.frame` class object
`split.field` | A character string of a recognized column name in `df` that contains the grouping. This column defines how the rows of `df` are split and is typically a `factor` or `character` vector. When `split.field` is not provided the `df` will be split by the number of rows.
`names.field` | An optional single `character` string indicating the name of the column in `df` that designates the names for the ranges in the elements of the GRangesList.
`...` | Additional arguments passed on to makeGRangesFromDataFrame

### Value

A GRangesList of the same length as the number of levels or unique character strings in the `df` column indicated by `split.field`. When `split.field` is not provided the `df` is split by row and the resulting GRangesList has the same length as nrow(df).

Names on the individual ranges are taken from the `names.field` argument. Names on the outer list elements of the GRangesList are propagated from `split.field`.

### Author(s)

M. Ramos

### See Also

- makeGRangesFromDataFrame

### Examples

    ## ---------------------------------------------------------------------
    ## BASIC EXAMPLES
    ## ---------------------------------------------------------------------

    df <- data.frame(chr="chr1", start=11:15, end=12:16,
                     strand=c("+","-","+","*","."), score=1:5,
                     specimen = c("a", "a", "b", "b", "c"),
                     gene_symbols = paste0("GENE", letters[1:5]))
    df

    grl <- makeGRangesListFromDataFrame(df, split.field = "specimen",
                                        names.field = "gene_symbols")
    grl
    names(grl)

    ## Keep metadata columns
    makeGRangesListFromDataFrame(df, split.field = "specimen",
                                 keep.extra.columns = TRUE)

[Package GenomicRanges version 1.36.1 Index]