gtrack.export_bedgraph: Export a track to bedGraph format

Description

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

Usage

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

Value

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

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.

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.

Examples

Run this code

if (FALSE) {
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")
}