Build a Matrix

This function converts various objects into a matrix format.

Usage

# S3 method for class 'MAF'
fortify_matrix(
  data,
  ...,
  genes = NULL,
  n_top = NULL,
  remove_empty_samples = TRUE,
  collapse_vars = TRUE,
  use_syn = TRUE
)

Arguments

data

An object to be converted to a matrix.

...

Not used currently.

genes

An atomic character defines the genes to draw.

n_top

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

remove_empty_samples

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

collapse_vars

A single boolean value indicating whether to collapse multiple alterations in the same sample and gene into a single value "Multi_Hit". Alternatively, you can provide a single string indicates the collapsed values.

use_syn

A single boolean value indicates whether to include synonymous variants when Classifies SNPs into transitions and transversions.

Value

A matrix.

ggalign attributes

• gene_summary: gene summary informations. See maftools::getGeneSummary() for details.

• sample_summary: sample summary informations. See maftools::getSampleSummary() for details.

• sample_anno: sample clinical informations. See maftools::getClinicalData() for details.

• n_genes: Total of genes.

• n_samples: Total of samples.

• titv: A list of data.frames with Transitions and Transversions summary. See maftools::titv() for details.

See also

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