long_to_matrix: Long to wide data format conversion

In symbioticMe/proBatch: Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Long to wide data format conversion

Description

Convert from a long data frame representation to a wide matrix representation

Usage

long_to_matrix(df_long, feature_id_col = "peptide_group_label",
  measure_col = "Intensity", sample_id_col = "FullRunName",
  qual_col = NULL, qual_value = 2)

Arguments

df_long	data frame where each row is a single feature in a single sample. It minimally has a sample_id_col, a feature_id_col and a measure_col, but usually also an m_score (in OpenSWATH output result file). See help("example_proteome") for more details.
feature_id_col	name of the column with feature/gene/peptide/protein ID used in the long format representation df_long. In the wide formatted representation data_matrix this corresponds to the row names.
measure_col	if df_long is among the parameters, it is the column with expression/abundance/intensity; otherwise, it is used internally for consistency.
sample_id_col	name of the column in sample_annotation table, where the filenames (colnames of the data_matrix are found).
qual_col	column to color point by certain value denoted by qual_value. Design with inferred/requant values in OpenSWATH output data, which means argument value has to be set to m_score.
qual_value	value in qual_col to color. For OpenSWATH data, this argument value has to be set to 2 (this is an m_score value for imputed values (requant values).

Value

data_matrix (proBatch) like matrix (features in rows, samples in columns)

See Also

Other matrix manipulation functions: matrix_to_long

Examples

proteome_matrix <- long_to_matrix(example_proteome)

symbioticMe/proBatch documentation built on April 9, 2023, 11:59 a.m.