export_ipath3: export_ipath3

In metaprotr: Metaproteomics Post-Processing Analysis

Description

Exports the KEGG Orthology (KO) terms in the adapted format to be used in the tool iPATH3. The exported data is obtained from a "spectral_count_object" containing the functional annotation of the identified proteins from one condition or sample.

Usage

export_ipath3(
  spectral_count_object,
  type_export,
  target_variable,
  sample_condition,
  hexadecimal_color,
  taxonomic_levels = NULL,
  force = FALSE
)

Arguments

spectral_count_object	List defined as "spectral_count_object" containing protein abundance expressed as spectral counts by a taxonomic level. The functional annotation must be added to this object. The format of this object is similar to that generated from the function "add_kegg".
type_export	Character indicating the type of export to be used. The possible options are: i) "all" that selects all the KO terms from a given sample or a given condition; and, ii) "selection" that extracts the KO terms present in selected taxonomic entities (one or more).
target_variable	Character indicating the column name from metadata containing the condition or sample to be analyzed.
sample_condition	Atomic vector indicating the sample from which the functional information will be extracted.
hexadecimal_color	Character indicating the color to be used in iPATH3, this value must be indicated in hexadecimal format (eg. #ff0000).
taxonomic_levels	Optional vector indicating the taxonomic levels from which the KO terms will be extracted. This option is needed only if the type of export is "selection".
force	Logic value set at FALSE by default in order to ask permission to create a file in the workstation of the user.

Value

A csv file containing the KO terms present in a given sample or condition. The content of this file can be inserted directly in the tool iPATH3. The width of the lines in iPATH3 will be displayed by the percentage of spectra in the selected sample or condition. In this way, KO terms belonging to a given taxonomic level are represented in three intervals based on their abundace: i) below 2 percent, i) between 2 to 10 percent, or i) above 10 percent.

Examples

data(species_annot_fw)

export_ipath3(
   species_annot_fw, 
   "all", 
   "SampleID", 
   "Q1_prot", 
   "#840AA3"
)

taxonomic_entities <- c("Bacteroides caccae", "Coprococcus catus", "Merdimonas faecis")
export_ipath3(
   species_annot_fw, 
   "selection", 
   "SC_name", 
   "FW2", 
   "#28c1df", 
   taxonomic_entities
)

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