omu_summary {omu} | R Documentation |
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")