create GRP2 configuration. Use this function if there is no Yaml Input.

Usage

make_DEA_config(
  ZIPDIR = ".",
  PROJECTID = "",
  ORDERID = "",
  WORKUNITID = "",
  Normalization = c("none", "vsn", "quantile", "robscale"),
  aggregation = c("medpolish", "top3", "lmrob"),
  Diffthreshold = 1,
  FDRthreshold = 0.1,
  removeContaminants = FALSE,
  removeDecoys = FALSE,
  patternDecoys = "^REV_",
  patternContaminants = "^zz",
  application = "FragPipeTMT",
  nrPeptides = 2
)

Arguments

ZIPDIR: output zip directory
PROJECTID: project identifier
ORDERID: order identifier
WORKUNITID: workunit identifier
Normalization: normalization method
aggregation: aggregation method
Diffthreshold: fold-change difference threshold
FDRthreshold: FDR significance threshold
removeContaminants: if TRUE remove contaminants
removeDecoys: if TRUE remove decoy sequences
patternDecoys: default "^REV_"
patternContaminants: default "^zz_"
application: software application name
nrPeptides: minimum number of peptides per protein

Examples

DEAconfig <- make_DEA_config()
#> Warning: DEPRECATED
DEAconfig
#> $project_spec
#> $project_spec$project_Id
#> [1] ""
#> 
#> $project_spec$project_name
#> [1] ""
#> 
#> $project_spec$order_Id
#> [1] ""
#> 
#> $project_spec$workunit_Id
#> [1] ""
#> 
#> 
#> $pop
#> $pop$transform
#> [1] "none"
#> 
#> $pop$aggregate
#> [1] "medpolish"
#> 
#> $pop$Diffthreshold
#> [1] 1
#> 
#> $pop$FDRthreshold
#> [1] 0.1
#> 
#> $pop$removeCon
#> [1] FALSE
#> 
#> $pop$removeDecoys
#> [1] FALSE
#> 
#> $pop$revpattern
#> [1] "^REV_"
#> 
#> $pop$contpattern
#> [1] "^zz"
#> 
#> $pop$nr_peptdes
#> [1] 2
#> 
#> 
#> $Software
#> [1] "FragPipeTMT"
#> 
#> $zipdir
#> [1] "."
#>