extract_bg: extract bg

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

extract bg

Description

A generic function to extract the background data for micro array data.

Usage

extract_bg(iden, data_files, genepix_vars = genepix_vars)

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.

Details

Extract the background values

Value

A data frame of background values

Examples

## 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)
extract_bg(iden ="KK2-06" , data_files=data_files,genepix_vars=genepix_vars)
## End(Not run)

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