array_vars: List the array structure variables

In Keniajin/protGear: Protein Micro Array Data Management and Interactive Visualization

List the array structure variables

Description

A generic function returning a list with the data structure.

Usage

array_vars(
  channel = "635",
  totsamples,
  FG = "",
  BG = "",
  FBG = "",
  blockspersample,
  chip_path = "data/array_data",
  sampleID_path = "data/array_sampleID/",
  mig_prefix = "_first",
  machine = "",
  date_process = ""
)

Arguments

channel	A character indicating the channel that the data was scanned at. It is mostly included in the MFI variable names.
totsamples	A numeric value indicating teh number of samples on a slide.
FG	Optional:A character indicating the name of the foreground variable name. if not specified its created as paste0("F",channel,".Median")
BG	Optional:A character indicating the name of the background variable name. if not specified its created as paste0("B",channel,".Median")
FBG	Optional:A character indicating the name of the foreground - background variable name. if not specified its created as paste0("F",channel,".Median...B",channel)
blockspersample	A numeric value indicating the numer of blocks in a mini-array. The ".gal" file can help in getting this
chip_path	A character indicating the path of the folder location with the array data.
sampleID_path	A character indicating the path of the folder location with the sample identifiers matching the array structure.
mig_prefix	Optional: A character indicating the identifier of an MIG dilution file
machine	Optional:A character indicating the machine used to process the data in the folder
date_process	Optional:A character indicating the date when the samples were processed.

Value

a list of parameters required to process the data

genepix_vars

Examples

## specify the the parameters to process the data
genepix_vars <- array_vars(
## the channel the data was processed in
  channel = "635",
  ## folder where the array data is stored
  chip_path = "data/array_data",
  ## the number of samples per slide or in as single run
  totsamples = 21,
  ## How many blocks each sample occupies
  blockspersample = 2,
  ## folder where the array data samples id files are stored
  sampleID_path = "data/array_sampleID/",
  ## optional
  mig_prefix = "_first",
  machine = 1,
  date_process = "0520"
)
genepix_vars

Keniajin/protGear documentation built on Feb. 6, 2023, 6:28 p.m.