metaprotr (version 1.2.2)

crumble_taxonomy: crumble_taxonomy

Description

Generates a list of four elements defined as "spectral_count_object" containing taxonomic classification. The first element is a dataset that contains the spectral counts abundance organized by a provided taxonomic level. The possible taxonomic levels are: species, genus, family, order, class, phylum or superkingdom.

Usage

crumble_taxonomy(spectral_count_object, taxonomic_level, filter_rate = 1)

Arguments

spectral_count_object

List defined as "spectral_count_object" containing dataframes with abundance expressed as spectral counts and organized by peptides, subgroups or groups. The format of this object is similar to that generated with the function "getsc_specific". Taxonomy must be added previously with "add_taxonomy" function.

taxonomic_level

Character indicating the taxonomic level to which the spectral abundance will be arranged in the samples of the "spectral_count_object". The possible options are: "species", "genus", "family", "order", "class", "phylum" or "superkingdom".

filter_rate

Numeric value between 0 and 1 that indicates the minimal rate of consensual annotation desired by the user within each level of the spectral category (subgroup or group). This rate is defined as the ratio between the number of the most frequent annotation entity ("species", "genus", "family", "order", "class", "phylum" or "superkingdom") divided by the total number of entities within each level of the spectral category under study (subgroup or group). The default value is set to 1, if 100 % of consensus is desired.

Value

A list of four elements defined as "spectral_count_object", the first element is a dataframe with abundance expressed as spectral counts of entities (peptides, subgroups or groups) organized by the provided taxonomic level. The second element is a dataframe that contains the experiment information. The third element is a dataframe containing the information of peptides with their associated proteins. And the fourth element is a character indicating the type of object generated.

Examples

# NOT RUN {
data(fecal_waters)

superkingdom_fecalwaters <- crumble_taxonomy(fecal_waters, "superkingdom")

phylum_fecalwaters <- crumble_taxonomy(fecal_waters, "phylum")

class_fecalwaters <- crumble_taxonomy(fecal_waters, "class")

order_fecalwaters <- crumble_taxonomy(fecal_waters, "order")

family_fecalwaters <- crumble_taxonomy(fecal_waters, "family")

genus_fecalwaters <- crumble_taxonomy(fecal_waters, "genus")

species_fecalwaters <- crumble_taxonomy(fecal_waters, "species")

# }