A generic function to extract the background data for micro array data.
extract_bg(iden, data_files, genepix_vars = genepix_vars)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 data frame of background values
Extract the background values
## Not run:
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"
)
#Define the data path
data_path <- paste0(genepix_vars$chip_path)
# List the file names to use
filenames <- list.files(genepix_vars$chip_path,
pattern = '*.txt$|*.gpr$', full.names = FALSE
)
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))
names(data_files)
#> [1] "BRB001" "KK2-06"
extract_bg(iden ="KK2-06" , data_files=data_files,genepix_vars=genepix_vars)
#> Warning: KK2-06 Not found in the sampleID files heredata/array_sampleID/
#> # A tibble: 7,245 × 6
#> # Groups: sampleID, antigen [2,415]
#> sampleID antigen Block FBG_Median BG_Median replicate
#> <chr> <chr> <int> <int> <int> <int>
#> 1 SID_gen1 MSP3.6 1 5488 1126 1
#> 2 SID_gen1 ETRAMP10.2 1 6350 1026 1
#> 3 SID_gen1 GAMA 1 15768 1059 1
#> 4 SID_gen1 MSRP4 1 65535 1413 1
#> 5 SID_gen1 MSP4 1 65535 1405 1
#> 6 SID_gen1 RAMA 1 43966 1085 1
#> 7 SID_gen1 ASP 1 65535 1092 1
#> 8 SID_gen1 MSP3.6 1 6596 1343 2
#> 9 SID_gen1 ETRAMP10.2 1 7123 1136 2
#> 10 SID_gen1 GAMA 1 17420 1311 2
#> # … with 7,235 more rows
## End(Not run)