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Methods for DeeDeeExperiment objects

Source: R/DeeDeeExperiment-methods.R
DeeDeeExperiment-methods.Rd

The DeeDeeExperiment() class provides a family of methods to get and set DE-related information and functional enrichment results in DeeDeeExperiment objects.

Usage

# S4 method for class 'DeeDeeExperiment'
dea_info(x)

# S4 method for class 'DeeDeeExperiment'
dea_info(x) <- value

# S4 method for class 'DeeDeeExperiment'
dea_names(x)

# S4 method for class 'DeeDeeExperiment'
rename_dea(x, old_name, new_name)

# S4 method for class 'DeeDeeExperiment'
add_dea(x, dea, force = FALSE)

# S4 method for class 'DeeDeeExperiment'
remove_dea(x, dea_name, remove_linked_fea = FALSE)

# S4 method for class 'DeeDeeExperiment'
dea(
  x,
  dea_name = NULL,
  format = "minimal",
  extra_rd = NULL,
  type = "DFrame",
  verbose = FALSE
)

# S4 method for class 'DeeDeeExperiment'
get_dea_list(x, format = "minimal", verbose = FALSE)

# S4 method for class 'DeeDeeExperiment'
add_scenario_info(x, dea_name, info = NULL, force = FALSE)

# S4 method for class 'DeeDeeExperiment'
fea_info(x)

# S4 method for class 'DeeDeeExperiment'
fea_info(x) <- value

# S4 method for class 'DeeDeeExperiment'
fea_names(x)

# S4 method for class 'DeeDeeExperiment'
rename_fea(x, old_name, new_name)

# S4 method for class 'DeeDeeExperiment'
add_fea(
  x,
  fea,
  de_name = NA_character_,
  fe_name = NULL,
  fea_tool = "auto",
  force = FALSE,
  verbose = FALSE
)

# S4 method for class 'DeeDeeExperiment'
remove_fea(x, fea_name)

# S4 method for class 'DeeDeeExperiment'
fea(x, fea_name = NULL, format = "minimal", verbose = FALSE)

# S4 method for class 'DeeDeeExperiment'
get_fea_list(x, dea_name = NULL, format = "minimal", verbose = FALSE)

# S4 method for class 'DeeDeeExperiment'
link_dea_and_fea(x, dea_name, fea_name, force = FALSE)

Arguments

x

A DeeDeeExperiment() object

value

Replacement value for replacement methods.

old_name

A character vector of existing DEA names to be renamed in a DeeDeeExperiment object

new_name

A character vector with new names to assign to existing DEA names in a DeeDeeExperiment object. It must be the same length of old_name, and contains unique values that don't overlap with existing DEA names.

dea

A named list of DE results, in any of the formats supported by the package (currently: results from DESeq2, edgeR, limma).

force

A logical, indicating whether to overwrite results when introducing the same results name. It defaults to FALSE.

dea_name

Character value, specifying the name of the DE analysis to get or remove, or match against (e.g., to fetch associated FEA results), or to which additional context and information can be attached

remove_linked_fea

A logical, specifying whether to remove or not the linked FEA when a DEA results is removed

format

A character string, specifying the DEA/FEAs output format. It takes either "minimal" to return only essential columns (e.g. log2FC, p-value, adjusted p-value for DEAs, or gs_id, gs_description, gs_pvalue, gs_genes... for FEAs), or "original" to return the full result object. It defaults to "minimal"

extra_rd

A character vector of additional columns from rowData(x) to include. It defaults to c("gene_id", "SYMBOL").

type

A character string referring to the type of object returned by dea(). It defaults to DFrame, but can also take the value of data.frame

verbose

Logical, whether or not to display warnings. If TRUE, warnings/messages will be displayed. If FALSE, the function runs silently

info

A character vector, containing contextual information about the specified DE analysis. It defaults to NULL

fea

A named list of Functional Enrichment results. Each element can be either a data.frame (currently supports results from topGO, enrichR, gProfiler, fgsea, gsea, DAVID, and output of GeneTonic shakers), or an enrichResult/gseaResult objects (currently supports clusterProfiler)

de_name

A character string to explicitly specify the name of the de result this fea should be linked to. If not provided, the function will attempt to match fea names to de results automatically.

fe_name

A character string giving a name to the FE results.

fea_tool

A character string indicating the FEA tool used. It can take any of the following values : "topGO", "clusterProfiler", "GeneTonic", "DAVID", "gsea", "fgsea", "enrichr", "gProfiler". When not specified, it defaults to "auto" and the tool is inferred automatically based on the input.

fea_name

Character value, specifying the name of the functional enrichment result to add or remove

Value

Return value varies depending on the individual methods, as described below.

Details

DEAs

  • dea_info and dea_info<- are the methods to get and set the dea information as a whole. These methods return DeeDeeExperiment objects.

  • dea_names returns the names of the available DE contrasts in DeeDeeExperiment objects.

  • rename_dea is the method to rename one or multiple DEAs stored in a DeeDeeExperiment object.

  • add_dea and remove_dea are used to respectively add or remove DE-results items. These methods also return DeeDeeExperiment objects, with updated content in the dea slot.

  • dea and get_dea_list retrieve the DEA information, as well as some extra rowData information and provide this as a DataFrame object (for a specific analysis) or as a list, with one element for each reported analysis.

  • add_scenario_info is the method to add user defined contextual information for a specific DE analysis. It allows users to attach free-text notes to a specific DEA results that stored in a DeeDeeExperiment object. This information can include any other relevant information to help document that DEA scenario. This context is stored in the dea slot under the name scenario_info, which is not a default element in dea.

FEAs

  • fea_info and fea_info<- are the methods to get and set the fea information as a whole. These methods return DeeDeeExperiment objects.

  • fea_names returns the names of the available enrichment results in DeeDeeExperiment objects.

  • rename_fea is the method to rename one or multiple FEAs stored in a DeeDeeExperiment object.

  • add_fea and remove_fea are used to respectively add or remove functional enrichment results items. These methods also return DeeDeeExperiment objects, with updated content in the fea slot.

  • fea is the method to retrieve FE results stored in a DeeDeeExperiment object for a specific contrast, as a standardized format similar to the output of GeneTonic shakers.

  • get_fea_list is the method that retrieves FEA results as a list. if the dea_name is indicated, the method will return only FEAs linked to that dea_name, otherwise it returns all FEAs in the fea slot.

  • link_dea_and_fea is the method that allows the user to manually link a FEA result to a specific DEA result.

  • show is the method to nicely print out the information of a DeeDeeExperiment object.

  • summary is the method to print a summary of the available DE and FE results in a DeeDeeExperiment object.

Examples

data("de_named_list", package = "DeeDeeExperiment")
data("topGO_results_list", package = "DeeDeeExperiment")
library("SummarizedExperiment")

rd_macrophage <- DataFrame(
  gene_id = rownames(de_named_list$ifng_vs_naive)
)
rownames(rd_macrophage) <- rownames(de_named_list$ifng_vs_naive)
se_macrophage_noassays <- SummarizedExperiment(
  assays = SimpleList(),
  rowData = rd_macrophage
)

# creating a `DeeDeeExperiment`
dde <- DeeDeeExperiment(
  se_macrophage_noassays,
  de_results = de_named_list
)
dde
#> class: DeeDeeExperiment 
#> dim: 1000 0 
#> metadata(1): version
#> assays(0):
#> rownames(1000): ENSG00000164741 ENSG00000078808 ... ENSG00000273680
#>   ENSG00000073536
#> rowData names(13): gene_id ifng_vs_naive_log2FoldChange ...
#>   salmo_both_pvalue salmo_both_padj
#> colnames: NULL
#> colData names(0):
#> dea(4): ifng_vs_naive, ifngsalmo_vs_naive, salmonella_vs_naive, salmo_both 
#> fea(0): 

new_del <- list(
  ifng2 = de_named_list$ifng_vs_naive,
  ifngsalmo2 = de_named_list$ifngsalmo_vs_naive
)

# add a new (set of) DE result(s)
dde_new <- add_dea(dde, new_del)
dde_new
#> class: DeeDeeExperiment 
#> dim: 1000 0 
#> metadata(1): version
#> assays(0):
#> rownames(1000): ENSG00000164741 ENSG00000078808 ... ENSG00000273680
#>   ENSG00000073536
#> rowData names(19): gene_id ifng_vs_naive_log2FoldChange ...
#>   ifngsalmo2_pvalue ifngsalmo2_padj
#> colnames: NULL
#> colData names(0):
#> dea(6): ifng_vs_naive, ifngsalmo_vs_naive, salmonella_vs_naive, salmo_both, ifng2, ifngsalmo2 
#> fea(0): 

# removing DEAs
dde_removed <- remove_dea(dde, "ifng_vs_naive")
dde_removed
#> class: DeeDeeExperiment 
#> dim: 1000 0 
#> metadata(1): version
#> assays(0):
#> rownames(1000): ENSG00000164741 ENSG00000078808 ... ENSG00000273680
#>   ENSG00000073536
#> rowData names(10): gene_id ifngsalmo_vs_naive_log2FoldChange ...
#>   salmo_both_pvalue salmo_both_padj
#> colnames: NULL
#> colData names(0):
#> dea(3): ifngsalmo_vs_naive, salmonella_vs_naive, salmo_both 
#> fea(0): 

# add a new (set of) FE result(s)
dde_new <- add_fea(dde, fea = topGO_results_list)
#> Found 955 gene sets in `topGOtableResult` object.
#> Converting for usage within the DeeDeeExperiment framework...
#> Found 955 gene sets in `topGOtableResult` object.
#> Converting for usage within the DeeDeeExperiment framework...
#> Found 955 gene sets in `topGOtableResult` object.
#> Converting for usage within the DeeDeeExperiment framework...
#> Found 955 gene sets in `topGOtableResult` object.
#> Converting for usage within the DeeDeeExperiment framework...

# removing FEAs
dde_rem <- remove_fea(dde_new, "ifng_vs_naive")

# display available DEAs
dea_names(dde)
#> [1] "ifng_vs_naive"       "ifngsalmo_vs_naive"  "salmonella_vs_naive"
#> [4] "salmo_both"         

# display available FEAs
fea_names(dde)
#> NULL

# print a summary of the available DEAs and FEAs
summary(dde, FDR = 0.01)
#> DE Results Summary:
#>             DEA_name  Up Down  FDR
#>        ifng_vs_naive  30   15 0.01
#>   ifngsalmo_vs_naive 104   29 0.01
#>  salmonella_vs_naive  80   29 0.01
#>           salmo_both  37   20 0.01
#> 
#> No FEA results stored.

# rename DEA
dde_new <- rename_dea(dde_new,
  old_name = "salmonella_vs_naive",
  new_name = "Salmo_vs_Naive_renamed"
)
#> ✔ Renamed DEA entries: "salmonella_vs_naive" to "Salmo_vs_Naive_renamed"

# assign DEA to FEA

dde_new <- link_dea_and_fea(dde_new,
  dea_name = "ifngsalmo_vs_naive",
  fea_name = "ifngsalmo_vs_naive"
)
#> ✔ Assigning DEA: "ifngsalmo_vs_naive" to FEA "ifngsalmo_vs_naive"