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

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", "lmrob"),
  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"
)

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", "lmrob"

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)

Value

ProlfquAppConfig R6 object

See also

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

Examples

DEAconfig <- make_DEA_config_R6(ORDERID = "1234", WORKUNITID = "1234")
DEAconfig$set_zipdir_name()
#> [1] "DEA_20260225_O1234_WU1234_none"
DEAconfig$get_zipdir()
#> [1] "./DEA_20260225_O1234_WU1234_none"
DEAconfig$get_result_dir()
#> [1] "./DEA_20260225_O1234_WU1234_none/Results_WU_1234"
DEAconfig$get_input_dir()
#> [1] "./DEA_20260225_O1234_WU1234_none/Inputs_WU_1234"
R6list <- prolfqua::R6_extract_values(DEAconfig)