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Two Sample T-test Comparisons. [Deprecated]

Source: R/cyt_ttest.R
cyt_ttest.Rd

This function performs pairwise comparisons between two groups for each combination of a categorical predictor (with exactly two levels) and a continuous outcome variable. It first converts any character variables in data to factors and, if specified, applies a shared scaling or transformation to the continuous variables. The function conducts a Shapiro-Wilk normality test to decide whether to use a Two-Sample T-Test vs. a Wilcoxon Rank Sum Test. The resulting p-values are printed and returned.

Usage

cyt_ttest(
  data,
  scale = NULL,
  format_output = FALSE,
  progress = NULL,
  custom_fn = NULL
)

Arguments

data

A matrix or data frame containing continuous and categorical variables.

scale

A character specifying a transformation for continuous variables. Options are NULL (default; no transformation), "none", "log2", "log10", "zscore", or "custom".

format_output

Logical. If TRUE, returns the results as a tidy data frame. Default is FALSE.

progress

Optional. A Shiny Progress object for reporting progress updates.

custom_fn

Optional transformation function used when scale = "custom".

Value

If format_output is FALSE, returns a list of p-values (named by Outcome and Categorical variable). If TRUE, returns a data frame with columns "Outcome", "Categorical", "Comparison", and "P_value".

Examples

data_df <- ExampleData1[, -c(3)]
data_df <- dplyr::filter(data_df, Group != "ND", Treatment != "Unstimulated")

cyt_ttest(data_df[, c(1, 2, 5:6)], scale = "log2", format_output = TRUE)
#> Warning: `cyt_ttest()` was deprecated in CytokineProfileShinyApp 0.0.1.
#> ℹ Please use `cyt_univariate()` instead.
#> $out_df
#>   Outcome Categorical      Comparison
#> 1   IFN.G       Group   PreT2D vs T2D
#> 2   IL.10       Group   PreT2D vs T2D
#> 3   IFN.G   Treatment CD3/CD28 vs LPS
#> 4   IL.10   Treatment CD3/CD28 vs LPS
#>                                                Test Estimate Statistic P_value
#> 1 Wilcoxon rank sum test with continuity correction   -2.463    1599.0   0.008
#> 2 Wilcoxon rank sum test with continuity correction   -0.956    1625.0   0.012
#> 3 Wilcoxon rank sum test with continuity correction    9.024    4132.5   0.000
#> 4 Wilcoxon rank sum test with continuity correction    1.690    3091.0   0.000
#>