SummarizeResult {QuICSeedR} | R Documentation |
Summarize Analysis Results
Description
This function combines analysis results from multiple tests with metadata, and determines overall significance based on a specified method. By default, it evaluates sample-level result by calculating the percentage of technical replicates that exceed the pre-defined threshold.
Usage
SummarizeResult(
analysis = NULL,
calculation,
sig_method = "xth_percent",
method_threshold = 50
)
Arguments
analysis |
Output of |
calculation |
Output of |
sig_method |
Specifies the approach for determining sample-level result. Available options include "xth_percent", "metric_count", "xth_count", or any metric name present in the analysis list. The default is "xth_percent". |
method_threshold |
Defines the threshold value for the "metric_count", "xth_count", and "xth_percent" methods. This parameter defaults to 50. |
Value
A data frame summarizing results of the analysis and calculation, with columns:
result: Overall result based on the chosen method
position: Location of the sample replications based on plate layout
method: Method chosen for determination of the result
*_sig: Significance indicator for each metric
*_p: P-value or adjusted p-value for each metric
metric_count: Count of significant results across all analyses
xth_count: The number of reactions crossing the fluorescent threshold
total_rep: Total number of replicates
xth_percent: Percentage of replicates crossing the fluorescent threshold
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, sd_fold = 10)
#Formatting calculations for analysis (also compatible with graphing softwares used in F-SAA
#research)
calculation_spread = SpreadCalculation(calculation)
#Get analysis comparing samples to negative control using the one-tailed Wilcox Rank-Sum test.
analysis <- GetAnalysis(calculation_spread, control = "Neg", test = "wilcox",
alternative = 'greater')
#Summarization of results. Default method is rate of amyloid formation.
result <- SummarizeResult(analysis, calculation)
head(result)