filter-ranges {plyranges} | R Documentation

## Subset a `Ranges` object

### Description

Subset a `Ranges` object

### Usage

    ## S3 method for class 'Ranges'
    filter(.data, ..., .preserve = FALSE)

### Arguments

`.data` | A `Ranges` object
`...` | valid logical predictates to subset .data by. These are determined by variables in `.data`. If more than one condition is supplied, the conditions are combined with `&`. Only rows where the condition evaluates to `TRUE` are kept.
`.preserve` | when FALSE (the default) grouping structure is recalculated, TRUE is currently not implemented.

### Details

For any Ranges objects `filter` can act on all core components of the class including start, end, width (for IRanges) or seqnames and strand (for GRanges) in addition to metadata columns. If the Ranges object is grouped, `filter` will act seperately on each parition of the data.

### Value

a Ranges object

### See Also

`dplyr::filter()`

### Examples

    set.seed(100)
    df <- data.frame(start = 1:10,
                     width = 5,
                     seqnames = "seq1",
                     strand = sample(c("+", "-", "*"), 10, replace = TRUE),
                     gc = runif(10))

    rng <- as_granges(df)

    filter(rng, strand == "+")
    filter(rng, gc > 0.5)

    # multiple criteria
    filter(rng, strand == "+" | start > 5)
    filter(rng, strand == "+" & start > 5)

    # multiple conditions are the same as and
    filter(rng, strand == "+", start > 5)

    # grouping acts on each subset of the data
    rng %>%
      group_by(strand) %>%
      filter(gc > 0.5)

[Package plyranges version 1.14.0 Index]