trans_func: Create trans_func object for functional analysis.

Description

This class is a wrapper for a series of functional analysis on species and communities, including the prokaryotes function identification based on Louca et al. (2016) <doi:10.1126/science.aaf4507> or fungi function identification based on Nguyen et al. (2016) <10.1016/j.funeco.2015.06.006>, functional redundancy calculation and metabolic pathway abundance prediction Abhauer et al. (2015) <10.1093/bioinformatics/btv287>.

Arguments

Active bindings

func_group_list: store and show the function group list

Methods

Public methods

Method `new()`

Usage

trans_func$new(dataset = NULL)

Arguments

dataset: the object of microtable Class.

Returns

for_what : "prok" or "fungi" or NA, "prok" represent prokaryotes. "fungi" represent fungi. NA represent not identified according to the Kingdom information, at this time, if you want to use the functions to identify species traits, you need provide "prok" or "fungi" manually, e.g. dataset$for_what <- "prok".

Examples

data(dataset)
t1 <- trans_func$new(dataset = dataset)

Method `cal_spe_func()`

Confirm traits of each OTU by matching the taxonomic assignments to the functional database; Prokaryotes: based on the FAPROTAX database, please also cite the original FAPROTAX paper: Louca, S., Parfrey, L. W., & Doebeli, M. (2016). Decoupling function and taxonomy in the global ocean microbiome. Science, 353(6305), 1272. <doi:10.1126/science.aaf4507>; Fungi, based on the FUNGuild database or FungalTraits database, please also cite: FUNGuild: Nguyen et al. (2016). FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild. Fungal Ecology, 20(1), 241-248, <doi:10.1016/j.funeco.2015.06.006> FungalTraits: Polme et al. FungalTraits: a user-friendly traits database of fungi and fungus-like stramenopiles. Fungal Diversity 105, 1-16 (2020). <doi:10.1007/s13225-020-00466-2>

Usage

trans_func$cal_spe_func(fungi_database = c("FUNGuild", "FungalTraits")[1])

Arguments

fungi_database: default "FUNGuild"; select a fungi trait database for the trait identification, "FUNGuild" or "FungalTraits"; see the description in this function.

Returns

res_spe_func in object.

Examples

\donttest{
t1$cal_spe_func()
}

Method `cal_spe_func_perc()`

Calculating the percentages of species with specific trait in communities or modules. The percentages of the OTUs with specific trait can reflect the potential of the corresponding function in the community or the module in the network.

Usage

trans_func$cal_spe_func_perc(
  use_community = TRUE,
  abundance_weighted = FALSE,
  node_type_table = NULL
)

Arguments

use_community: default TRUE; whether calculate community; if FALSE, use module.

abundance_weighted

default FALSE; whether use abundance. If FALSE, calculate the functional population percentage. If TRUE, calculate the functional individual percentage.

node_type_table

default NULL; If use_community FALSE; provide the node_type_table with the module information, such as the result of cal_node_type.

Returns

res_spe_func_perc in object.

Examples

\donttest{
t1$cal_spe_func_perc(use_community = TRUE)
}

Method `show_prok_func()`

Show the basic information for a specific function of prokaryotes.

Usage

trans_func$show_prok_func(use_func = NULL)

Arguments

use_func: default NULL; the function name.

Returns

None.

Examples

\donttest{
t1$show_prok_func(use_func = "methanotrophy")
}

Method `plot_spe_func_perc()`

Plot the percentages of species with specific trait in communities or modules.

Usage

trans_func$plot_spe_func_perc(
  filter_func = NULL,
  use_group_list = TRUE,
  add_facet = TRUE,
  select_samples = NULL
)

Arguments

filter_func: default NULL; a vector of function names used to show in the plot.

use_group_list

default TRUE; If TRUE, use default group list; If use personalized group list, first set trans_func$func_group_list object with a list of group names and functions.

add_facet

default TRUE; whether use group names as the facets in the plot, see trans_func$func_group_list object.

select_samples

default NULL; character vector, select partial samples to show

Returns

ggplot2.

Examples

\donttest{
t1$plot_spe_func_perc(use_group_list = TRUE)
}

Method `cal_tax4fun()`

Predict functional potential of communities using tax4fun. please also cite: Tax4Fun: Predicting functional profiles from metagenomic 16S rRNA data. Bioinformatics, 31(17), 2882-2884, <doi:10.1093/bioinformatics/btv287>

Usage

trans_func$cal_tax4fun(keep_tem = FALSE, folderReferenceData = NULL)

Arguments

keep_tem: default FALSE; whether keep the intermediate file, that is, the otu table in local place.

folderReferenceData

default NULL; the folder, see http://tax4fun.gobics.de/ and Tax4Fun function in Tax4Fun package.

Returns

tax4fun_KO and tax4fun_path in object.

Method `cal_tax4fun2()`

Predict functional potential of communities with Tax4Fun2 method. please also cite: Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. Environmental Microbiome 15, 11 (2020). <doi:10.1186/s40793-020-00358-7>

Usage

trans_func$cal_tax4fun2(
  blast_tool_path = NULL,
  path_to_reference_data = "Tax4Fun2_ReferenceData_v2",
  path_to_temp_folder = NULL,
  database_mode = "Ref99NR",
  normalize_by_copy_number = T,
  min_identity_to_reference = 97,
  use_uproc = T,
  num_threads = 1,
  normalize_pathways = F
)

Arguments

blast_tool_path: default NULL; the folder path, e.g. ncbi-blast-2.11.0+/bin ; blast tools folder downloaded from "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+" ; e.g. ncbi-blast-2.11.0+-x64-win64.tar.gz for windows system; if blast_tool_path is NULL, search the tools in the environmental path variable.

path_to_reference_data

default "Tax4Fun2_ReferenceData_v2"; the path that points to files used in the prediction; The directory must contain the Ref99NR/Ref100NR folder; download Ref99NR.zip from "https://cloudstor.aarnet.edu.au/plus/s/DkoZIyZpMNbrzSw/download" or Ref100NR.zip from "https://cloudstor.aarnet.edu.au/plus/s/jIByczak9ZAFUB4/download" .

path_to_temp_folder

default NULL; The temporary folder to store the logfile, intermediate file and result files; if NULL, use the default temporary in the computer.

database_mode

default 'Ref99NR'; "Ref99NR" or "Ref100NR" .

normalize_by_copy_number

default TRUE; whether normalize the result by the 16S rRNA copy number in the genomes.

min_identity_to_reference

default 97; the idenity threshold used for finding the nearest species.

use_uproc

default TRUE; UProC was used to functionally anotate the genomes in the reference data.

num_threads

default 1; the threads used in the blastn calculation.

normalize_pathways

default FALSE; Different to Tax4Fun, when converting from KEGG functions to KEGG pathways, Tax4Fun2 does not equally split KO gene abundances between pathways a functions is affiliated to. The full predicted abundance is affiliated to each pathway. Use TRUE to split the abundances (default is FALSE).

Returns

res_tax4fun2_KO and res_tax4fun2_pathway in object.

Examples

\dontrun{
t1$cal_tax4fun2(blast_tool_path = "ncbi-blast-2.11.0+/bin", 
    path_to_reference_data = "Tax4Fun2_ReferenceData_v2")
}

Method `cal_tax4fun2_FRI()`

Calculate (multi-) functional redundancy index (FRI) of prokaryotic community with Tax4Fun2 method. This function is used to calculating aFRI and rFRI use the intermediate files generated by the function cal_tax4fun2(). please also cite: Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. Environmental Microbiome 15, 11 (2020). <doi:10.1186/s40793-020-00358-7>

Usage

trans_func$cal_tax4fun2_FRI()

Returns

res_tax4fun2_aFRI and res_tax4fun2_rFRI in object.

Examples

\dontrun{
t1$cal_tax4fun2_FRI()
}

Method `print()`

Print the trans_func object.

Usage

trans_func$print()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

trans_func$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples

Run this code

# NOT RUN {
## ------------------------------------------------
## Method `trans_func$new`
## ------------------------------------------------

data(dataset)
t1 <- trans_func$new(dataset = dataset)

## ------------------------------------------------
## Method `trans_func$cal_spe_func`
## ------------------------------------------------

# }
# NOT RUN {
t1$cal_spe_func()
# }
# NOT RUN {
## ------------------------------------------------
## Method `trans_func$cal_spe_func_perc`
## ------------------------------------------------

# }
# NOT RUN {
t1$cal_spe_func_perc(use_community = TRUE)
# }
# NOT RUN {
## ------------------------------------------------
## Method `trans_func$show_prok_func`
## ------------------------------------------------

# }
# NOT RUN {
t1$show_prok_func(use_func = "methanotrophy")
# }
# NOT RUN {
## ------------------------------------------------
## Method `trans_func$plot_spe_func_perc`
## ------------------------------------------------

# }
# NOT RUN {
t1$plot_spe_func_perc(use_group_list = TRUE)
# }
# NOT RUN {
## ------------------------------------------------
## Method `trans_func$cal_tax4fun2`
## ------------------------------------------------

# }
# NOT RUN {
t1$cal_tax4fun2(blast_tool_path = "ncbi-blast-2.11.0+/bin", 
    path_to_reference_data = "Tax4Fun2_ReferenceData_v2")
# }
# NOT RUN {
## ------------------------------------------------
## Method `trans_func$cal_tax4fun2_FRI`
## ------------------------------------------------

# }
# NOT RUN {
t1$cal_tax4fun2_FRI()
# }

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Description

Arguments

Active bindings

Methods

Public methods

Method new()

Usage

Arguments

Returns

Examples

Method cal_spe_func()

Usage

Arguments

Returns

Examples

Method cal_spe_func_perc()

Usage

Arguments

Returns

Examples

Method show_prok_func()

Usage

Arguments

Returns

Examples

Method plot_spe_func_perc()

Usage

Arguments

Returns

Examples

Method cal_tax4fun()

Usage

Arguments

Returns

Method cal_tax4fun2()

Usage

Arguments

Returns

Examples

Method cal_tax4fun2_FRI()

Usage

Returns

Examples

Method print()

Usage

Method clone()

Usage

Arguments

Examples

Method `new()`

Method `cal_spe_func()`

Method `cal_spe_func_perc()`

Method `show_prok_func()`

Method `plot_spe_func_perc()`

Method `cal_tax4fun()`

Method `cal_tax4fun2()`

Method `cal_tax4fun2_FRI()`

Method `print()`

Method `clone()`