filter_shared: filter_shared

In metaprotr: Metaproteomics Post-Processing Analysis

Description

Keeps the elements from a "spectral_count_object" that are common to all levels of a provided explanatory variable. This variable MUST correspond to the name of ONE column of the dataframe "metadata" (eg. conditions or samples). This function allows to identify the elements that are common to several conditions or samples.

Usage

filter_shared(spectral_count_object, metadata_feature)

Arguments

spectral_count_object	List containing dataframes with proteomics elements whose abundance is expressed as spectral counts and are organized by peptides, subgroups, groups or taxonomic levels. The format of this object is similar to that generated from the functions "getsc_specific" and "crumble_taxonomy".
metadata_feature	Character indicating the name of one explanatory variable (ONE column name) of the dataframe "metadata".

Value

A list defined as "spectral_count_object" in which the elements (groups, subgroups, peptides or taxonomic levels) of a given variable (condition or samples) from metadata will have at least ONE spectra per variable.

Examples

data(fecal_waters)
data(species_fw)

common_elements_per_sample <- filter_shared(fecal_waters, "SampleID")

common_elements_per_condition <- filter_shared(species_fw, "Condition")

metaprotr documentation built on Feb. 5, 2021, 9:06 a.m.