long_to_matrix {proBatch}R Documentation

Long to wide 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")

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)

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 file, where the filenames (colnames of the data matrix are found)

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)


[Package proBatch version 1.0.0 Index]