GetCalculation {QuICSeedR}R Documentation

Perform Calculations

Description

This function takes cleaned raw data and performs various analyses, including calculating the time to threshold, Rate of Amyloid Formation (RAF), Max Point Ratio (MPR), Max Slope (MS), and whether the reaction crosses the threshold (XTH).

Usage

GetCalculation(
  raw,
  meta,
  norm = FALSE,
  norm_ct,
  threshold_method = "stdv",
  time_skip = 5,
  sd_fold = 3,
  bg_fold = 3,
  rfu = 5000,
  cycle_background = 4,
  binw = 6
)

Arguments

raw

Cleaned raw data matrix. Output from CleanRaw().

meta

Cleaned meta data. Output from CleanMeta().

norm

Logical. If TRUE, normalization will be performed. Default is FALSE.

norm_ct

Sample name used to normalize calculation.

threshold_method

Method for calculating threshold ('stdv', 'rfu_val', or 'bg_ratio').

time_skip

Number of initial time points to skip when checking for threshold crossing. This helps ignore early crossings that may be due to reasons unrelated to seeding activity.

sd_fold

Fold of standard deviation to calculate the threshold for RAF (for 'stdv' method).

bg_fold

Background fold for threshold calculation (for 'bg_ratio' method).

rfu

Relative fluorescence unit values used for threshold (for 'rfu_val' method).

cycle_background

The cycle number chosen as the background for RAF and MPR calculations.

binw

Bin width for the MS calculation.

Value

A data frame containing the results of the calculation.

References

Henderson DM, Davenport KA, Haley NJ, Denkers ND, Mathiason CK, Hoover EA. Quantitative assessment of prion infectivity in tissues and body fluids by real-time quaking-induced conversion. J Gen Virol. 2015;96(Pt 1):210-219. doi:10.1099/vir.0.069906-0

Li M, Schwabenlander MD, Rowden GR, Schefers JM, Jennelle CS, Carstensen M, Seelig D, Larsen PA. RT-QuIC detection of CWD prion seeding activity in white-tailed deer muscle tissues. Sci Rep. 2021;11(1):16759. doi: 10.1038/s41598-021-96127-8. PMID: 34408204; PMCID: PMC8373970.

Rowden GR, Picasso-Risso C, Li M, Schwabenlander MD, Wolf TM, Larsen PA. Standardization of Data Analysis for RT-QuIC-Based Detection of Chronic Wasting Disease. Pathogens. 2023;12(2):309. doi:10.3390/pathogens12020309

Haley NJ, Van de Motter A, Carver S, et al. Prion-seeding activity in cerebrospinal fluid of deer with chronic wasting disease. PLoS One. 2013;8(11):e81488. doi:10.1371/journal.pone.0081488

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 
cleanraw <- CleanRaw(meta, raw, plate_time)

#Get calculations using positive controls to normalize values. 
calculation = GetCalculation(raw = cleanraw, meta, norm = TRUE, norm_ct = 'Pos')

head(calculation)


[Package QuICSeedR version 0.1.2 Index]