omu (version 1.1.2)

omu_summary: 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

c57_nos2KO_mouse_countDF <- c57_nos2KO_mouse_countDF[1:12,]
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")