setup_ideograms: Setup ideograms
In teunbrand/ggnomics: ggnomics

Description Usage Arguments Details Value Methods (by class) See Also Examples

Sets up a local cache of ideogram data for a genome.

setup_ideograms(
  data = NULL,
  genome = NULL,
  colourmap = default_ideogram_colours()
)

data

One of the following:

A data.frame with the following 6 columns:

chrom
A character column with chromosome names.

chromStart
An integer vector with band start positions.

chromEnd
An integer vector with band end positions.

name
A character with names for cytogenetic bands.

gieStain
A character with Giemsa stain results. Recognised values are: "gneg", "gpos", "gpos50", "gpos75", "gpos25", "gpos100", "acen", "gvar", and "stalk".
A character with the filename from which the data are to be read from.
Can be missing if the genome argument is set. See details.

genome

A character with the genome name, e.g. "mm10".

colourmap

A named character vector with colours where names correspond to the gieStain column.

If the data argument is missing but the genome argument is either "hg19", "hg38", "mm9" or "mm10", BiocFileCache is used to cache the cytoBand.txt file from UCSC.

Returns no value, but caches the ideograms under the genome identifier in a temporary cache.

data = data.frame,genome = ANY: Uses data.frame to generate ideograms
data = character,genome = ANY: Uses character as file path.
data = missing_OR_NULL,genome = character: Attempts to lookup genome in UCSC tables and caches this.