omu_summary: omu_summary Performs comparison of means between two...

In omu: A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection

omu_summary Performs comparison of means between two independent variables, standard deviation, standard error, FDR correction, fold change, log2FoldChange. The order effects the fold change values

Description

omu_summary Performs comparison of means between two independent variables, standard deviation, standard error, FDR correction, fold change, log2FoldChange. The order effects the fold change values

Usage

omu_summary(
  count_data,
  metadata,
  numerator,
  denominator,
  response_variable = "Metabolite",
  Factor,
  log_transform = FALSE,
  p_adjust = "BH",
  test_type = "welch",
  paired = FALSE
)

Arguments

count_data	should be a metabolomics count data frame
metadata	is meta data
numerator	is the variable you wish to compare against the denominator, in quotes
denominator	see above, in quotes
response_variable	the name of the column with your response variables
Factor	the column name for your independent variables
log_transform	TRUE or FALSE value for whether or not log transformation of data is performed before the t test
p_adjust	Method for adjusting the p value, i.e. "BH"
test_type	One of "mwu", "students", or "welch" to determine which model to use
paired	A boolean of TRUE or FALSE. If TRUE, performs a paired sample test. To perform a paired sample test, metadata must have a column named 'ID' containing the subject IDs.

Examples

omu_summary(count_data = c57_nos2KO_mouse_countDF, metadata = c57_nos2KO_mouse_metadata,
numerator = "Strep", denominator = "Mock", response_variable = "Metabolite", Factor = "Treatment",
log_transform = TRUE, p_adjust = "BH", test_type = "welch")

omu documentation built on Oct. 17, 2023, 1:06 a.m.