center_peptide_batch_medians {proBatch} | R Documentation |
Median centering of the peptides (per batch median)
center_peptide_batch_medians(df_long, sample_annotation = NULL, sample_id_col = "FullRunName", batch_col = "MS_batch", feature_id_col = "peptide_group_label", measure_col = "Intensity")
df_long |
data frame where each row is a single feature in a single
sample. It minimally has a |
sample_annotation |
data frame with sample ID, technical (e.g. MS batches) and biological (e.g. Diet) covariates |
sample_id_col |
name of the column in sample_annotation file, where the filenames (colnames of the data matrix are found) |
batch_col |
column in |
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
-size long format data with batch-effect corrected with
per-feature batch median centering in Intensity_normalized column
median_centered_proteome <- center_peptide_batch_medians( example_proteome, example_sample_annotation)