transform_raw_data: Functions to log transform raw data before normalization and...

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

Functions to log transform raw data before normalization and batch correction

Description

Functions to log transform raw data before normalization and batch correction

Log transformation of the data

"Unlog" transformation of the data to pre-log form (for quantification, forcing log-transform)

Usage

log_transform_df(df_long, log_base = 2, offset = 1,
  measure_col = "Intensity")

unlog_df(df_long, log_base = 2, offset = 1,
  measure_col = "Intensity")

log_transform_dm(data_matrix, log_base = 2, offset = 1)

unlog_dm(data_matrix, log_base = 2, offset = 1)

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.
log_base	base of the logarithm for transformation
offset	small positive number to prevent 0 conversion to -Inf
measure_col	if df_long is among the parameters, it is the column with expression/abundance/intensity; otherwise, it is used internally for consistency.
data_matrix	features (in rows) vs samples (in columns) matrix, with feature IDs in rownames and file/sample names as colnames. See "example_proteome_matrix" for more details (to call the description, use help("example_proteome_matrix"))

Value

'log_transform_df()' returns df_long-size data frame, with measure_col log transformed; with old value in another column called "beforeLog_intensity" if "intensity" was the value of measure_col; 'log_transform_dm()' returns data_matrix format matrix

Examples

log_transformed_df <- log_transform_df(example_proteome)

log_transformed_matrix <- log_transform_dm(example_proteome_matrix, 
log_base = 10, offset = 1)

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