ProjectStructure: keep track of folder paths and create them if needed

In wolski/prolfqua: Proteomics Label Free Quantification

keep track of folder paths and create them if needed

Description

keep track of folder paths and create them if needed

keep track of folder paths and create them if needed

Public fields

outpath

path

qc_dir

qc results directory name

modelling_dir

modeling results directory name

project_Id

project_Id

order_Id

order_Id

workunit_Id

workunit_Id

inputData

inputFile

inputAnnotation

inputAnnotation xlsx

Methods

Public methods

• ProjectStructure$new()

• ProjectStructure$create_outpath()

• ProjectStructure$qc_path()

• ProjectStructure$modelling_path()

• ProjectStructure$create()

• ProjectStructure$reset()

• ProjectStructure$clone()

---

Method new()

create ProjectStructure

Usage

ProjectStructure$new(
  outpath,
  project_Id,
  order_Id,
  workunit_Id,
  inputAnnotation,
  inputData,
  qc_dir = "qc_results",
  modelling_dir = "modelling_results"
)

Arguments

outpath

directory

project_Id

bfabric project ID

order_Id

bfabric order_Id

workunit_Id

bfabric workunit_Id

inputAnnotation

input annotation path

inputData

input data path

qc_dir

qc folder

modelling_dir

modelling results folder

---

Method create_outpath()

create outpath

Usage

ProjectStructure$create_outpath()

---

Method qc_path()

create qc dir

Usage

ProjectStructure$qc_path(qc_dir)

Arguments

qc_dir

QC directory

---

Method modelling_path()

create modelling path

Usage

ProjectStructure$modelling_path(modelling_dir)

Arguments

modelling_dir

directory with modelling data

---

Method create()

create all directories

Usage

ProjectStructure$create()

---

Method reset()

empty modelling_path and qc_path folder.

Usage

ProjectStructure$reset()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ProjectStructure$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

tmp <- ProjectStructure$new("./test_project",
project_Id  = 3000,
order_Id = 6200,
workunit_Id = 23000,
inputAnnotation = ".",
inputData = "."
)
tmp$qc_path()
tmp$modelling_path()

tmp$modelling_path()
tmp$modelling_dir
tmp$modelling_path("second_model")
tmp$create()
tmp$reset()

wolski/prolfqua documentation built on May 12, 2024, 10:16 p.m.