identify_differences {metaprotr}

identify_differences

Description

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.

Usage

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

Arguments

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.

Value

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.

Examples

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)