GenomicRanges: makeGRangesListFromDataFrame – R documentation

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makeGRangesListFromDataFrame

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

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)

GenomicRanges

Representation and manipulation of genomic intervals

v1.42.0

Artistic-2.0

Authors

P. Aboyoun, H. Pagès, and M. Lawrence

Initial release