metaprotr (version 1.2.2)

filter_text: filter_text

Description

Matches the entities containing a given chain of characters inside an explanatory variable (column name) of the dataframe "peptides_proteins" from a "spectral_count_object". Based on the user's decision, the peptides, subgroups, groups or taxonomic levels containig the provided chain of characters will be kept or discarted in a newly generated object.

Usage

filter_text(spectral_count_object, pepsprots_feature, text_to_filter, decision)

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".

pepsprots_feature

Character indicating the name of one explanatory variable (ONE column name) of the dataframe "peptides_proteins".

text_to_filter

Character containig the text to be searched in the "pepsprots_feature" content.

decision

Character indicating wether the elements containing the matched text will be kept or dirscarted. The two allowed option are: "keep" or "discard".

Value

A list defined as "spectral_count_object" with or without the elements (peptides, subgroups, groups, taxonomic items) that matched the provided text in a given variable of the "peptides_proteins" dataframe.

Examples

# NOT RUN {
data(fecal_waters)
data(species_fw)

cysteine_alkylations <- filter_text(fecal_waters, "Modifs", "57.02146", "keep")

exclude_medimonas <- filter_text(species_fw, "organism", "Merdimonas faecis BR31", "discard")

# }