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)A character indicating the name of the object to be used under data_files.
A list of data objects with names utilised by iden.
A list of specific definitions of the experiment design.
See array_vars.
A description of the background correction to be used.
See bg_correct.
a data frame merged with corresponding sample ID's. The sample ID are specified in the sample ID files
## 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 ¹sample_array_ID, ²BGMedian, ³FMedianBG_correct, ⁴replicate
## End(Not run)