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Build a Matrix

Source: R/fortify-matrix.R
fortify_matrix.GISTIC.Rd

This function converts various objects into a matrix format.

Usage

# S3 method for class 'GISTIC'
fortify_matrix(
  data,
  ...,
  n_top = NULL,
  bands = NULL,
  ignored_bands = NULL,
  sample_anno = NULL,
  remove_empty_samples = TRUE
)

Arguments

data

An object to be converted to a matrix.

...

Not used currently.

n_top

A single number indicates how many top bands to be drawn.

bands

An atomic character defines the bands to draw.

ignored_bands

An atomic character defines the bands to be ignored.

sample_anno

A data frame of sample clinical features to be added.

remove_empty_samples

A single boolean value indicating whether to drop samples without any genomic alterations.

Value

A matrix.

ggalign attributes

  • sample_anno: sample clinical informations provided in sample_anno.

  • sample_summary: sample copy number summary informations. See data@cnv.summary for details.

  • cytoband_summary: cytoband summary informations. See data@cytoband.summary for details.

  • gene_summary: gene summary informations. See data@gene.summary for details.

  • summary: A data frame of summary information. See data@summary for details.

See also

Other fortify_matrix methods: fortify_matrix.MAF(), fortify_matrix.default()