Package 'gDR'

Title: Umbrella package for R packages in the gDR suite
Description: Package is a part of the gDR suite. It reexports functions from other packages in the gDR suite that contain critical processing functions and utilities. The vignette walks through the full processing pipeline for drug response analyses that the gDR suite offers.
Authors: Allison Vuong [aut], Bartosz Czech [aut] , Arkadiusz Gladki [cre, aut] , Marc Hafner [aut] , Dariusz Scigocki [aut], Janina Smola [aut], Sergiu Mocanu [aut]
Maintainer: Arkadiusz Gladki <[email protected]>
License: Artistic-2.0
Version: 1.3.1
Built: 2024-06-29 02:16:44 UTC
Source: https://github.com/bioc/gDR

Help Index

Import raw data

Description

Import raw data

Usage

import_data(
  manifest_file,
  template_file,
  results_file,
  instrument = "EnVision"
)

Arguments

manifest_file

character, file path(s) to manifest(s)
template_file

character, with datapaths and names of results file(s) or character with file path of templates file(s)
results_file

character, with datapaths and names of results file(s) or character with file path of results file(s)
instrument

string with type of instrument used

Value

a data.table

Examples

td <- get_test_data()
i_df <- import_data(manifest_path(td), template_path(td), result_path(td))

Small data.table with raw combo data used for processing via gDR

Description

A dataset containing the ReadoutValues for combo experiments made-up of 3 drugs, 2 co-drugs, and 2 cell lines

Usage

data(small_combo_data)

Format

A data frame with 3600 rows and 16 variables:

Barcode

barcode

clid

cell line id

CellLineName

cell line name

Tissue

cell line tissue

ReferenceDivisionTime

cell line division time

Gnumber

drug id

DrugName

drug name

drug_moa

drug mode of action

Concentration

drug concentration

Gnumber_2

co-drug id

DrugName_2

co-drug name

drug_moa_2

co-drug mode of action

Concentration_2

co-drug concentration

ReadoutValue

readout value

BackgroundValue

backgroud value

Duration

duration

Value

data.table

Small data.table with raw data used for processing via gDR

Description

A dataset containing the ReadoutValues for single-agent experiments made-up of 10 drugs and 10 cell lines

Usage

data(small_data)

Format

A data frame with 3300 rows and 12 variables:

Barcode

barcode

clid

cell line id

CellLineName

cell line name

Tissue

cell line tissue

ReferenceDivisionTime

cell line division time

Gnumber

drug id

DrugName

drug name

drug_moa

drug mode of action

Concentration

drug concentration

ReadoutValue

readout value

BackgroundValue

backgroud value

Duration

duration

Value

data.table