tag_subtract: tag_subtract

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

tag_subtract

Description

\\_End_Function_\\ #

Usage

tag_subtract(
  dataC_mfi,
  tag_antigens,
  mean_best_CV_var,
  tag_file,
  batch_vars,
  sampleID_var = "sampleID",
  antigen_var = "antigen"
)

Arguments

dataC_mfi	A dataframe
tag_antigens	A character vector with the names of proteins or antigens used as TAG.
mean_best_CV_var	A character string containing the identifier of the variable with the MFI values.
tag_file	A data frame with variables antigen, TAG, TAG_name to show the TAG for the different antigens or proteins in dataC_mfi
batch_vars	A list of characters identifying variables in dataC_mfi for indicating batch.
sampleID_var	A character string containing the name of the sample identifier variable. Default set to 'sampleID'
antigen_var	A character string containing the name of the features/protein variable. Default to 'antigen'

Details

Subtract the purification TAG data

Value

A data frame of TAG values subtracted

Examples

tag_file <- readr::read_csv(system.file("extdata", "TAG_antigens.csv", 
package="protGear"))
tag_antigens <- c("CD4TAG", "GST", "MBP")
batch_vars <- list(machine = "m1", day = "0520")
dataC <- readr::read_csv(system.file("extdata", "dataC.csv",
 package="protGear"))
## this file has 3 lab replicates and the default names
dataCV <- cv_estimation(dataC  ,lab_replicates=3)
dataCV_best2 <- best_CV_estimation(dataCV,slide_id = "iden", 
lab_replicates = 3, cv_cut_off = 20)
tag_subtract(dataCV_best2,tag_antigens=tag_antigens, 
mean_best_CV_var="mean_best_CV",
 tag_file = tag_file,antigen_var = "antigen", batch_vars = batch_vars)

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