matrix_to_long {proBatch}R Documentation

Wide to long conversion

Description

Convert from wide matrix to a long data frame representation

Usage

matrix_to_long(data_matrix, sample_annotation = NULL,
  feature_id_col = "peptide_group_label", measure_col = "Intensity",
  sample_id_col = "FullRunName", step = NULL)

Arguments

data_matrix

features (in rows) vs samples (in columns) matrix, with feature IDs in rownames and file/sample names as colnames. Usually the log transformed version of the original data

sample_annotation

data matrix with:

  1. sample_id_col (this can be repeated as row names)

  2. biological covariates

  3. technical covariates (batches etc)

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)

step

normalization step (e.g. Raw or Quantile_normalized or qNorm_ComBat). Useful if consecutive steps are compared in plots. Note that in plots these are usually ordered alphabetically, so it's worth naming with numbers, e.g. 1_raw, 2_quantile

Value

df_long (proBatch) like data frame

See Also

Other matrix manipulation functions: long_to_matrix

Examples

proteome_long <- matrix_to_long(example_proteome_matrix, 
example_sample_annotation)


[Package proBatch version 1.0.0 Index]