GetAnalysis {QuICSeedR}R Documentation

Perform Statistical Analysis on Calculations

Description

This function performs statistical analysis on a list of calculation spreads, comparing each column to a control column using various statistical tests.

Usage

GetAnalysis(
  calculation_spread,
  control,
  test = "wilcox",
  alternative = "two.sided",
  adjust_p = FALSE,
  alpha = 0.05
)

Arguments

calculation_spread

A list of data frames, each representing a calculation spread.

Output of SpreadCaculation().

control

The name or pattern of the control column in each data frame.

test

The statistical test to use. Options are:

  • "t-test": Student's t-test, suitable for normally distributed data. For more information, run: ?stats::t.test

  • "wilcox": Wilcoxon rank-sum test (also known as Mann-Whitney U test), a non-parametric test. For more information, run: ?stats::wilcox.test

  • "yuen": Yuen's test for trimmed means, robust against outliers and non-normality. For more information, run: ?WRS2::yuen

Default is "wilcox".

alternative

Options are "two.sided", "less", or "greater". Default is "two.sided".

adjust_p

Logical. Whether to adjust p-values for multiple comparisons. Default is FALSE.

alpha

The significance level for determining significance stars. Default is 0.05.

Value

A list of data frames containing the results of the statistical analysis for selected metrics.

References

Mair, P., & Wilcox, R. (2020). WRS2: A Collection of Robust Statistical Methods. https://CRAN.R-project.org/package=WRS2

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)

analysis <- GetAnalysis(calculation_spread, control = "Neg", test = "wilcox", 
                        alternative = 'greater')
head(analysis)


[Package QuICSeedR version 0.1.2 Index]