read_data {ceas}

Read Seahorse Wave Excel File

Description

Reads input seahore data from an excel Seahorse Wave File. It assumes your data is background normalized.

Usage

read_data(rep_list, norm = NULL, sheet = 2, delimiter = " ")

Arguments

rep_list

A list of Seahorse Wave excel export files. One file per replicate. If your data is in a directory called "seahorse_data", use list.files("seahorse_data", pattern = "*.xlsx", full.names = TRUE) to make a list of the excel files.

norm

A csv file with the experimental groups and their normalization values. Leave unset if normalization is not required. See normalize().

sheet

The number of the excel sheet containing the long-form Seahorse data. Default is 2 because the long-form output from Seahorse Wave is on sheet 2

delimiter

The delimiter between the group name and the assay type in the Group column of the wave output. e.g. "Group1 MITO" would use a space character as delimiter.

Value

a seahorse_rates table

Examples

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

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