gtrack.export_bedgraph: Export a track to bedGraph format

In misha: Toolkit for Analysis of Genomic Data

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
)

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.

Value

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

See Also

gextract, gtrack.export_bigwig, gtrack.info

Examples

## Not run: 
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")

## End(Not run)

misha documentation built on Aug. 24, 2026, 5:14 p.m.