Subset a Ranges object

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.

Value

a Ranges object

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.

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 == "+")
#> GRanges object with 1 range and 1 metadata column:
#>       seqnames    ranges strand |        gc
#>          <Rle> <IRanges>  <Rle> | <numeric>
#>   [1]     seq1       5-9      + |  0.357525
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
filter(rng, gc > 0.5)
#> GRanges object with 6 ranges and 1 metadata column:
#>       seqnames    ranges strand |        gc
#>          <Rle> <IRanges>  <Rle> | <numeric>
#>   [1]     seq1       2-6      * |  0.762551
#>   [2]     seq1       3-7      - |  0.669022
#>   [3]     seq1      7-11      - |  0.690291
#>   [4]     seq1      8-12      * |  0.535811
#>   [5]     seq1      9-13      - |  0.710804
#>   [6]     seq1     10-14      - |  0.538349
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

# multiple criteria
filter(rng, strand == "+" | start > 5)
#> GRanges object with 6 ranges and 1 metadata column:
#>       seqnames    ranges strand |        gc
#>          <Rle> <IRanges>  <Rle> | <numeric>
#>   [1]     seq1       5-9      + |  0.357525
#>   [2]     seq1      6-10      - |  0.359475
#>   [3]     seq1      7-11      - |  0.690291
#>   [4]     seq1      8-12      * |  0.535811
#>   [5]     seq1      9-13      - |  0.710804
#>   [6]     seq1     10-14      - |  0.538349
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths
filter(rng, strand == "+" & start > 5)
#> GRanges object with 0 ranges and 1 metadata column:
#>    seqnames    ranges strand |        gc
#>       <Rle> <IRanges>  <Rle> | <numeric>
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

# multiple conditions are the same as and
filter(rng, strand == "+", start > 5)
#> GRanges object with 0 ranges and 1 metadata column:
#>    seqnames    ranges strand |        gc
#>       <Rle> <IRanges>  <Rle> | <numeric>
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

# grouping acts on each subset of the data
rng %>%
  group_by(strand) %>%
  filter(gc > 0.5)
#> GRanges object with 6 ranges and 1 metadata column:
#> Groups: strand [2]
#>       seqnames    ranges strand |        gc
#>          <Rle> <IRanges>  <Rle> | <numeric>
#>   [1]     seq1       2-6      * |  0.762551
#>   [2]     seq1       3-7      - |  0.669022
#>   [3]     seq1      7-11      - |  0.690291
#>   [4]     seq1      8-12      * |  0.535811
#>   [5]     seq1      9-13      - |  0.710804
#>   [6]     seq1     10-14      - |  0.538349
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths