create GRP2 configuration for differential expression analysis Use this function if there is no Yaml Input.

Description

create GRP2 configuration for differential expression analysis Use this function if there is no Yaml Input.

Usage

make_DEA_config_R6(
  PATH = ".",
  PROJECTID = "",
  ORDERID = "",
  WORKUNITID = "",
  Normalization = c("none", "vsn", "quantile", "robscale"),
  aggregation = c("medpolish", "top3", "rlm"),
  diff_threshold = 1,
  FDR_threshold = 0.1,
  nr_peptides = 1,
  removeContaminants = FALSE,
  removeDecoys = FALSE,
  patternDecoys = "^REV_|^rev_",
  patternContaminants = "^zz|^CON|Cont_",
  application = "DIANN",
  prefix = "DEA",
  model = "lm_impute"
)

Arguments

PATH	working directory path
PROJECTID	project identifier
ORDERID	order identifier
WORKUNITID	workunit identifier
Normalization	normalization method: "none", "vsn", "quantile", "robscale"
aggregation	aggregation method: "medpolish", "top3", "rlm"
diff_threshold	difference threshold
FDR_threshold	FDR threshold
nr_peptides	number of peptides required
removeContaminants	should contaminants be removed
removeDecoys	should decoys be removed
patternDecoys	pattern for decoy proteins
patternContaminants	pattern for contaminant proteins
application	software application name
prefix	analysis prefix (DEA or QC)
model	facade registry key for contrast analysis. Use "saint" for SAINTexpress interaction scoring.

Value

ProlfquAppConfig R6 object

See Also

Other ProlfquAppConfig: ExternalReader, ProcessingOptions, ProjectSpec, ProlfquAppConfig, set_list_to_R6()

Examples

library("prolfquapp")


DEAconfig <- make_DEA_config_R6(ORDERID = "1234", WORKUNITID = "1234")
DEAconfig$set_zipdir_name()

[1] "DEA_20260729_O1234_WU1234_none"

DEAconfig$get_zipdir()

[1] "./DEA_20260729_O1234_WU1234_none"

DEAconfig$get_result_dir()

[1] "./DEA_20260729_O1234_WU1234_none/Results_WU_1234"

DEAconfig$get_input_dir()

[1] "./DEA_20260729_O1234_WU1234_none/Inputs_WU_1234"

R6list <- prolfqua::R6_extract_values(DEAconfig)