fwrite_igv: Write IGV file from intervals set data frame

In tanaylab/misha.ext: A home to functions that extend the misha package

Write IGV file from intervals set data frame

Description

Write IGV file from intervals set data frame

Usage

fwrite_igv(
  data,
  file,
  type = NULL,
  rm_intervalID = TRUE,
  feature_name = 1,
  ...
)

Arguments

data	data frame with chrom,start,end and additional data columns
file	name of the output IGV file
type	data type for IGV viewer. Available options are: COPY_NUMBER, GENE_EXPRESSION, CHIP, DNA_METHYLATION, ALLELE_SPECIFIC_COPY_NUMBER, LOH, RNAI. Note that if type is set other viewer options (in ...) would be ignored.
rm_intervalID	remove intervalID column from data
feature_name	feature name for IGV viewer
...	track parameters for IGV viewer. See: http://software.broadinstitute.org/software/igv/TrackLine.

Examples

## Not run: 
fwrite_igv(d, "out.igv", graphType = "points")
fwrite_igv(d, "out.igv", type = "DNA_METHYLATION")

## End(Not run)

tanaylab/misha.ext documentation built on Sept. 18, 2024, 2:53 a.m.