List the array structure variables — array_vars • protGear
Description: A generic function returning a list with the data structure.

# List the array structure variables

Source: `R/global_functions.R`
`array_vars.Rd`

A generic function returning a list with the data structure.

    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
    #> $FG
    #> F635.Median
    #>
    #> $BG
    #> B635.Median
    #>
    #> $FBG
    #> F635.Median...B635
    #>
    #> $paths
    #> character(0)
    #>
    #> $chip_path
    #> [1] "data/array_data"
    #>
    #> $sampleID_path
    #> [1] "data/array_sampleID/"
    #>
    #> $mig_prefix
    #> [1] "_first"
    #>
    #> $machine
    #> [1] 1
    #>
    #> $date_process
    #> [1] "0520"
    #>
    #> $totsamples
    #> [1] 21
    #>
    #> $blockspersample
    #> [1] 2
    #>
    #> $mp
    #> [1] 1
    #>
    #> $dp
    #> [1] "0520"
    #>