CleanRaw: Generate Clean Raw Data

In QuICSeedR: Analyze Data for Fluorophore-Assisted Seed Amplification Assays

Generate Clean Raw Data

Description

This function takes metadata, raw data, and total cycle information to generate clean raw fluorescence data.

Usage

CleanRaw(meta, raw, plate_time, cycle_total)

Arguments

meta	A data frame containing the metadata. Output from CleanMeta function.
raw	Raw fluorescence readings from MARS software.
plate_time	Output of ConvertTime().
cycle_total	The total number of cycles (rows) to include in the output.

Value

A data frame containing the cleaned raw fluorescence data.

Examples

# Define the path to the plate data file
plate_path <- system.file("extdata/20240716_p3", 
                          file = '20240716_p3_plate.xlsx', 
                          package = "QuICSeedR")
  
# Read the plate data
plate <- readxl::read_xlsx(plate_path)

# Define the path to the raw data file
raw_path <- system.file("extdata/20240716_p3", 
                        file = '20240716_p3_raw.xlsx', 
                        package = "QuICSeedR")
# Read the raw data
raw <- readxl::read_xlsx(raw_path)

# Get replicate data
replicate <- GetReplicate(plate)

# Ensure time displayed as decimal hours
plate_time = ConvertTime(raw)

#Get metadata and display the few rows 
meta = CleanMeta(raw, plate, replicate)

#Clean data 
cleaned_data <- CleanRaw(meta, raw, plate_time)

cleaned_data[1:5, 1:5]

QuICSeedR documentation built on Sept. 11, 2024, 8:21 p.m.