identify_differences: identify_differences
In metaprotr: Metaproteomics Post-Processing Analysis

Description Usage Arguments Value Examples

View source: R/metaprotr_identify_differences.R

Shows the most differential taxonomic elements between two conditions or samples from a list defined as "spectral_count_object" with taxonomic classification. These elements are those with an absolute log2 (condition + 1 / reference + 1) > 3. If a given condition has several replicates the mean value is taken into account.

identify_differences(
  spectral_count_object,
  target_variable,
  list_conditions,
  filter_ratio = 3,
  force = FALSE
)

`spectral_count_object`	List defined as "spectral_count_object" containing dataframes with abundance expressed as spectral counts and organized by taxonomic levels. The format of this object is similar to that generated from the function "crumble_taxonomy".
`target_variable`	Character indicating the variable name containing the conditions or samples to be compared. This value corresponds to the name of one column from metadata.
`list_conditions`	Atomic vector indicating two conditions to be compared. The first element will be considered as the reference.
`filter_ratio`	Numeric value indicating the fold change filter to be considered for the pairwise comparison. The minimal value can be a fold change of 1.25. The default value is set at 3.
`force`	Logic value set at FALSE by default in order to ask permission to create an object in the workstation of the user.

Barplots (pdf) and a csv file with the defferential taxonomic elements between TWO conditions or sample. These elements are those that fulfill the ratio log2 (condition + 1 / reference + 1) > filter_ratio.

data(species_fw)
identify_differences(species_fw, "Methods", c("S", "S_EF"))

identify_differences(species_fw, "Methods", c("EF", "S_EF"), filter_ratio = 1.3)