normalize_matrix: Normalize a numeric matrix; in MS-DAP this is typically a...

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

Normalize a numeric matrix; in MS-DAP this is typically a peptide-level log2 intensity matrix

Description

wrapper function around various normalization algorithms. In the results, log2 intensity values below 1 are thresholded at 1

Usage

normalize_matrix(
  x_as_log2,
  algorithm,
  group_by_cols = NA,
  group_by_rows = NA,
  rollup_algorithm = "maxlfq"
)

Arguments

x_as_log2	the numeric matrix, must be log2 transformed
algorithm	the normalization algorithm to apply. Either one of the built-in options, see normalization_algorithms function focumentation, or the name of your custom normalization function (see GitHub documentation on custom normalization functions for more details)
group_by_cols	a character array of the same length as the number of columns in the provided data matrix, describing the grouping of each column/sample
group_by_rows	optionally, an array of grouping IDs for the rows. e.g. if input matrix is a peptide table these can be strings with protein-group identifiers. Required parameter for modebetween_protein normalization
rollup_algorithm	optionally, the algorithm for combining peptides to proteins as used in normalization algorithms that require a priori rollup from peptides to a protein-level abundance matrix (e.g. modebetween_protein). Refer to rollup_pep2prot function documentation for available options and a brief description of each

See Also

normalization_algorithms() for available normalization algorithms and documentation.

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.