metaprotr (version 1.2.2)

remove_element: remove_element

Description

Removes elements from a "spectral_count_object". These elements can be: i) samples, ii) peptides, iii) proteins, iv) soubgroups, v) groups, vi) sequences, vii) species, viii) genus, ix) family, x) order, xi) class, xii) phylum or xiii) superkingdom.

Usage

remove_element(spectral_count_object, target_variable, list_elements)

Arguments

spectral_count_object

List defined as "spectral_count_object" containing dataframes with abundance expressed as spectral counts from peptides, subgroups, groups or taxonomic levels. The format of this object is similar to that generated from the functions "getsc_specific" and "crumble_taxonomy."

target_variable

Character indicating the variable that contains the elements to be removed. The options are : i) "peptides", ii) "proteins", iii) "soubgroups", iv) "groups", v) "sequences", vi) "species", vii) "genus", viii) "family", ix) "order", x) "class", xi) "phylum" or xii) "superkingdom". To select xiii) "samples", it should be indicated the name of ONE column from metadata.

list_elements

Atomic vector indicating the elements to be removed. For "samples", indicate the element(s) present in the provided variable from metadata. For "peptides", "proteins", "subgroups" and "groups" provide the X!Tandem nomenclature. For "sequences", provide the peptide sequences expressed as aminoacids. For any taxonomic level, provide the taxonomic entities.

Value

A list defined as "spectral_count_object" without the elements provided in the second argument of the function.

Examples

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

data_selected_samples <- remove_element(fecal_waters, "Methods", c("S_EF", "EF"))

data_selected_peptides <- remove_element(fecal_waters, "peptides", c("pepa3c417", "pepd4664a1"))

data_selected_proteins <- remove_element(species_fw, "proteins", c("a3.a9.a1", "a5.b81.a1"))

data_selected_subgroups <- remove_element(species_fw, "subgroups", c("a3.a9", "b73.a5"))

data_selected_groups <- remove_element(species_fw, "groups", c("a3", "b34", "c231"))

data_selected_sequences <- remove_element(species_fw, "sequences", c("AQLNFGGTIENVVIRDEFPLEK"))

# }