normalize {ceas}

Normalize Seahorse data

Description

Normalizes input data according to cell number or \mug of protein. It assumes your data is background normalized.

Usage

normalize(seahorse_rates, norm_csv)

Arguments

seahorse_rates

The seahorse rates table read by the read_data() function.

norm_csv

A csv file with the experimental groups in column 1 and cell count or \mug of protein in column 2. Headers are ignored.

Details

This normalization is distinct from the background normalization done by the Wave software. If the data are not background normalized, read_data() will output a warning showing rows with OCR, ECAR and PER values greater than 0.

Value

a normalzed seahorse_rates data.table

Examples

rep_list <- system.file("extdata", package = "ceas") |>
  list.files(pattern = "*.xlsx", full.names = TRUE)
norm_csv <- system.file("extdata", package = "ceas") |>
  list.files(pattern = "norm.csv", full.names = TRUE)
read.csv(norm_csv)
seahorse_rates <- read_data(rep_list, sheet = 2)
head(seahorse_rates, n = 10)
seahorse_rates.normalized <- normalize(seahorse_rates, norm_csv)
head(seahorse_rates.normalized, n = 10)