Extract a log2 fold-change matrix

Returns a gene-by-comparison matrix of log2 fold changes stored in a VISTA object.

Usage

get_foldchange_matrix(
  x,
  sample_comparisons = NULL,
  genes = NULL,
  display_id = NULL,
  display_from = NULL,
  display_orgdb = NULL
)

Arguments

x

A VISTA object containing differential expression results.

sample_comparisons

Optional character vector of comparison names. Defaults to all available comparisons.

genes

Optional character vector of gene identifiers. When omitted, all genes present in row_data(x) are returned. May be given as display labels when display_id is set.

display_id

Optional rowData() column (or annotation key) naming the labels to work in, matching get_foldchange_heatmap(). When supplied, genes is accepted in those labels and the returned matrix is labelled with them. Identifiers with no label keep their original value.

display_from

Identifier type rownames(x) are in, used only when display_id is not a rowData() column and the mapping goes through an annotation package.

display_orgdb

An OrgDb used for that mapping.

Value

A numeric matrix with genes in rows and comparisons in columns. Rows keep the object's gene identifiers unless display_id is supplied. Because display labels need not be unique, duplicates are made unique with a warning so that every row stays addressable by name.

Examples

v <- example_vista()
mat <- get_foldchange_matrix(v)
dim(mat)
#> [1] 123   1