Merge sample ID with the array data — merge_sampleID • protGear
Description: A generic function that merges the protein data with the sample identifiers or sample names. If the file does not have sample identifiers the function generates it automatically.

# Merge sample ID with the array data

Source: `R/read_files_functions.R`
`merge_sampleID.Rd`

A generic function that merges the protein data with the sample identifiers or sample names. If the file does not have sample identifiers the function generates it automatically.

    merge_sampleID(iden, data_files, genepix_vars, method)

## Arguments

iden

  A character indicating the name of the object to be used under data_files.

data_files

  A list of data objects with names utilised by iden.

genepix_vars

  A list of specific definitions of the experiment design. See `array_vars`.

method

  A description of the background correction to be used. See `bg_correct`.

## Value

a data frame merged with corresponding sample ID's. The sample ID are specified in the sample ID files

## Examples

    ## Not run:
    ### Define the genepix_vars
    genepix_vars <- array_vars(
      channel = "635",
      chip_path = system.file("extdata", "array_data/machine1/",
       package="protGear"),
      totsamples = 21,
      blockspersample = 2,
      mig_prefix = "_first",
      machine = 1,
      ## optional
      date_process = "0520"
    )

    ## the path where the micro-array data is located
    data_path <- paste0(genepix_vars$chip_path)
    filenames <- list.files(genepix_vars$chip_path,
                            pattern = "*.txt$|*.gpr$", full.names = FALSE
    )
    ## create a list of all the files
    data_files <- purrr::map(
     .x = filenames,
      .f = read_array_files,
      data_path = data_path,
      genepix_vars = genepix_vars
    )
    data_files <- purrr::set_names(data_files,
    purrr::map(filenames, name_of_files))
    ## merge the lab data with samples and perform bg correction
    merge_sampleID(iden = "KK2-06", data_files = data_files,
                   genepix_vars =genepix_vars,method = "subtract_global" )
    #> Warning: KK2-06.csv Not found in the sampleID filesdata/array_sampleID/
    #> # A tibble: 8,064 × 11
    #> # Groups:   sampleID, antigen [2,457]
    #>    sampleID sample_…¹ antigen FMedian BGMed…² FMedi…³ Block Column   Row repli…⁴
    #>    <chr>        <int> <chr>     <int>   <int>   <dbl> <int>  <int> <int>   <int>
    #>  1 SID_gen1         1 Landma…   65535    2443   64413     1      1     1       1
    #>  2 SID_gen1         1 MSP3.6     5488    1126    4366     1      2     1       1
    #>  3 SID_gen1         1 ETRAMP…    6350    1026    5228     1      3     1       1
    #>  4 SID_gen1         1 GAMA      15768    1059   14646     1      4     1       1
    #>  5 SID_gen1         1 MSRP4     65535    1413   64413     1      5     1       1
    #>  6 SID_gen1         1 MSP4      65535    1405   64413     1      6     1       1
    #>  7 SID_gen1         1 RAMA      43966    1085   42844     1      7     1       1
    #>  8 SID_gen1         1 ASP       65535    1092   64413     1      8     1       1
    #>  9 SID_gen1         1 Landma…   65535    4198   64413     1      1     2       2
    #> 10 SID_gen1         1 MSP3.6     6596    1343    5474     1      2     2       2
    #> # … with 8,054 more rows, 1 more variable: iden <chr>, and abbreviated variable
    #> #   names ¹​sample_array_ID, ²​BGMedian, ³​FMedianBG_correct, ⁴​replicate
    ## End(Not run)