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Export DEA/FEA/ASSAY results from a DeeDeeExperiment to excel files

Source: R/DeeDeeExperiment-internal-utils.R
export_result_for_dde.Rd

Extracts DEA and/or FEA results stored in a DeeDeeExperiment and writes them to excel files. Each contrast/result is written to a separate sheet. DEA and FEA are written to separate files.

Usage

export_result_for_dde(
  x,
  res_type = c("assay", "dea", "fea", "all"),
  res_format = c("minimal", "original"),
  output_dir = getwd(),
  file_name = NULL,
  assay_type = c("counts"),
  force = FALSE
)

Arguments

x

A DeeDeeExperiment object containing DEA/FEA results to be extracted

res_type

A character vector indicating the result to extract (i.e. "dea", "fea", "assay") from the corresponding slot If set to "all", DEAs, FEAs, as well as the specified assays are extracted into separate excel files

res_format

A character string specifying the DEA/FEAs output format to be exported (i.e. "minimal" or "original")

output_dir

A character string specifying the directory where the excel file will be written

file_name

Optional character string specifying a file name. If NULL, a default name is generated

assay_type

Optional character vector specifying the assays to export. It defaults to "counts"

force

Logical. If TRUE, an existing file with the same name will be overwritten

Value

An (invisible) character vector of file paths to the exported excel files. The vector may contain one path res_type = "dea" or res_type = "fea" or three paths res_type = "all"

Examples

data("de_named_list", package = "DeeDeeExperiment")
data("topGO_results_list", package = "DeeDeeExperiment")
dde <- DeeDeeExperiment(de_results = de_named_list, enrich_results = topGO_results_list)
#> ℹ creating a mock SCE from the rows of the DE result objects, if available
#> ℹ FEA "ifng_vs_naive" matched directly to DE contrast "ifng_vs_naive"
#> Found 955 gene sets in `topGOtableResult` object.
#> Converting for usage within the DeeDeeExperiment framework...
#> ℹ FEA "ifngsalmo_vs_naive" matched directly to DE contrast "ifngsalmo_vs_naive"
#> Found 955 gene sets in `topGOtableResult` object.
#> Converting for usage within the DeeDeeExperiment framework...
#> ℹ FEA "salmonella_vs_naive" matched directly to DE contrast "salmonella_vs_naive"
#> Found 955 gene sets in `topGOtableResult` object.
#> Converting for usage within the DeeDeeExperiment framework...
#> ℹ FEA "salmo_both" matched directly to DE contrast "salmo_both"
#> Found 955 gene sets in `topGOtableResult` object.
#> Converting for usage within the DeeDeeExperiment framework...

export_result_for_dde(dde,
res_type = "dea",
res_format = "minimal", output_dir = tempdir(), force = TRUE)
#> Found 4 DEA results
#> Writing results to: /var/folders/5q/v_ms_h9x6mv05dzlf94g48d00000gn/T//Rtmph5BxFT/dde_minimal_DEA.xlsx

export_result_for_dde(dde,
res_type = c("dea", "fea"),
res_format = "original", output_dir = tempdir(), force = TRUE)
#> Error in match.arg(res_type): 'arg' must be of length 1