Export a track to bedGraph format

Exports a track or track expression to a UCSC bedGraph file.

gtrack.export_bedgraph(
  track,
  file,
  intervals = NULL,
  iterator = NULL,
  name = NULL
)

Arguments

track

track name or track expression (character string)

file

output file path. If it ends in .gz, output is gzip-compressed.

intervals

genomic intervals to export. If NULL (default), the entire genome (.misha$ALLGENOME) is used.

iterator

iterator bin size. If NULL (default), the iterator is determined automatically from the track expression.

name

track name for the bedGraph header line. If NULL (default), uses the track parameter value.

Value

NULL (invisible). Called for its side effect of writing a file.

Details

This function evaluates a track expression over the specified genomic intervals and writes the result in standard bedGraph format (4-column, tab-separated: chrom, start, end, value). NaN values are omitted from the output.

The function supports physical tracks, virtual tracks, and arbitrary track expressions (e.g. "dense_track * 2"). 2D tracks are not supported.

If the output file path ends in .gz, the output is gzip-compressed.

See also

gextract, gtrack.export_bigwig, gtrack.info

Examples

if (FALSE) { # \dontrun{
gdb.init_examples()

# Export a dense track
gtrack.export_bedgraph("dense_track", "/tmp/dense.bedgraph")

# Export with specific intervals
intervs <- gintervals(1, 0, 1000)
gtrack.export_bedgraph("dense_track", "/tmp/dense_chr1.bedgraph",
    intervals = intervs
)

# Export a track expression
gtrack.export_bedgraph("dense_track * 2", "/tmp/scaled.bedgraph",
    iterator = 100
)

# Export compressed
gtrack.export_bedgraph("dense_track", "/tmp/dense.bedgraph.gz")
} # }