Write IGV file from intervals set data frame

Write IGV file from intervals set data frame

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

if (FALSE) {
fwrite_igv(d, "out.igv", graphType = "points")
fwrite_igv(d, "out.igv", type = "DNA_METHYLATION")
}