Read growth and fluorescence data in table format

read_data reads table files or R dataframe objects containing growth and fluorescence data and extracts datasets, sample and group information, performs blank correction, applies data transformation (calibration), and combines technical replicates.

Usage

read_data(
  data.growth = NA,
  data.fl = NA,
  data.fl2 = NA,
  data.format = "col",
  csvsep = ";",
  dec = ".",
  csvsep.fl = ";",
  dec.fl = ".",
  csvsep.fl2 = ";",
  dec.fl2 = ".",
  sheet.growth = 1,
  sheet.fl = 1,
  sheet.fl2 = 1,
  fl.normtype = c("growth", "fl2"),
  subtract.blank = TRUE,
  convert.time = NULL,
  calib.growth = NULL,
  calib.fl = NULL,
  calib.fl2 = NULL
)

Arguments

data.growth

An R dataframe object or a table file with extension '.xlsx', '.xls', '.csv', '.tsv', or '.txt' containing growth data. The data must be either in the 'QurvE custom layout' or in 'tidy' (long) format. The first three table rows in the 'custom QurvE layout' contain:

Sample description
Replicate number (optional: followed by a letter to indicate technical replicates)
Concentration value (optional)

Data in 'tidy' format requires the following column headers:

"Time": time values
"Description": sample description
"Replicate": replicate number (optional)
"Concentration": concentration value (optional)
"Values": growth values (e.g., optical density)

data.fl

(optional) An R dataframe object or a table file with extension '.xlsx', '.xls', '.csv', '.tsv', or '.txt' containing fluorescence data. Table layout must mimic that of data.growth.

data.fl2

(optional) An R dataframe object or a table file with extension '.xlsx', '.xls', '.csv', '.tsv', or '.txt' containing measurements from a second fluorescence channel (used only to normalize fluorescence data). Table layout must mimic that of data.growth.

data.format

(Character) "col" for samples in columns, or "row" for samples in rows. Default: "col"

csvsep

(Character) separator used in CSV file storing growth data (ignored for other file types). Default: ";"

dec

(Character) decimal separator used in CSV, TSV or TXT file storing growth data. Default: "."

csvsep.fl, csvsep.fl2

(Character) separator used in CSV file storing fluorescence data (ignored for other file types). Default: ";"

dec.fl, dec.fl2

(Character) decimal separator used in CSV, TSV or TXT file storing fluorescence data. Default: "."

sheet.growth, sheet.fl, sheet.fl2

(Numeric or Character) Number or name of the sheet with the respective data type in XLS or XLSX files (optional).

fl.normtype

(Character string) Normalize fluorescence values by either diving by 'growth' or by fluorescence2 values ('fl2').

subtract.blank

(Logical) Shall blank values be subtracted from values within the same experiment (TRUE, the default) or not (FALSE).

convert.time

(NULL or string) Convert time values with a formula provided in the form 'y = function(x)'. For example: convert.time = 'y = 24 * x'

calib.growth, calib.fl, calib.fl2

(Character or NULL) Provide an equation in the form 'y = function(x)' (for example: 'y = x^2 * 0.3 - 0.5') to convert growth and fluorescence values. This can be used to, e.g., convert plate reader absorbance values into OD₆₀₀ or fluorescence intensity into molecule concentrations. Caution!: When utilizing calibration, carefully consider whether or not blanks were subtracted to determine the calibration before selecting the input subtract.blank = TRUE.

Value

An R list object of class grodata containing a time matrix, dataframes with growth and fluorescence data (if applicable), and an experimental design table. The grodata object can be directly used to run growth.workflow/fl.workflow or, together with a growth.control/fl.control

object, in growth.gcFit/flFit.

time: Matrix with raw time values extracted from data.growth.
growth: Dataframe with raw growth values and sample identifiers extracted from data.growth.
fluorescence: Dataframe with raw fluorescence values and sample identifiers extracted from data.fl. NA, if no fluorescence data is provided.
norm.fluorescence: fluorescence data divided by growth values. NA, if no fluorescence data is provided.
expdesign: Experimental design table created from the first three identifier rows/columns (see argument data.format) (data.growth.

Details

Examples

# Load CSV file containing only growth data
data_growth <- read_data(data.growth = system.file("2-FMA_toxicity.csv",
                         package = "QurvE"), csvsep = ";" )
#> Sample data are stored in columns. If they are stored in row format, please run read_data() with data.format = 'row'.

# Load XLSX file containing both growth and fluorescence data
data_growth_fl <- read_data(data.growth = system.file("lac_promoters.xlsx", package = "QurvE"),
                            sheet.growth = "OD",
                            data.fl = system.file("lac_promoters.xlsx", package = "QurvE"),
                            sheet.fl = 2)
#> Sample data are stored in columns. If they are stored in row format, please run read_data() with data.format = 'row'.