frequency_matrix2nmat: Convert frequency matrix to normalizedMatrix format

In jmw86069/platjam: Platform Jam, biological platform importers.

Convert frequency matrix to normalizedMatrix format

Description

Convert frequency matrix to normalizedMatrix format

Usage

frequency_matrix2nmat(
  mat,
  target_frequency = NULL,
  target_name = "target",
  signal_name = "Frequency",
  do_scale = TRUE,
  scale_from = 0,
  scale_to = 1,
  scale_frequency = NULL,
  apply_floor = TRUE,
  verbose = FALSE,
  ...
)

Arguments

mat	numeric matrix with frequency represented as columns, and whose numeric frequency is stored in colnames(mat) as character values.
target_frequency	numeric vector representing a range of frequencies to be considered the "target", and thus highlighted by EnrichedHeatmap::EnrichedHeatmap(). By default the target range is used to order rows from high to low signal, unless the order is specified otherwise. When target_frequency is NULL, there is no target indicated in the normalizedMatrix.
...	additional arguments are ignored.

Details

This function takes input data with frequency represented as columns, and observations as rows. It will optionally scale each row to have fixed minimum-to-maximum value range, given a range of frequencies to use for scaling.

Value

normalizedMatrix object, a subclass of matrix, as defined in EnrichedHeatmap.

See Also

Other jam import functions: coverage_matrix2nmat(), deepTools_matrix2nmat(), import_lipotype_csv(), import_metabolomics_niehs(), import_nanostring_csv(), import_nanostring_rcc(), import_nanostring_rlf(), import_omics_data(), import_proteomics_PD(), import_proteomics_mascot(), import_salmon_quant(), process_metab_compounds_file()

jmw86069/platjam documentation built on Sept. 26, 2024, 3:31 p.m.