prepLum: Reformat raw luminex files for processing
In EPPIcenter/flexfit: Flexible Format Standard Curve Fitting and Data Processing

View source: R/prep.R

prepLum

R Documentation

Reformat raw luminex files for processing

Description

Read in raw luminex files, extract standards and background (if provided), and format samples for processing.

Usage

prepLum(
  antigen,
  fname,
  fdir = NULL,
  dtype = "Median",
  stdstr = "std|stand",
  bgstr = "blank|background",
  stddil = NULL,
  smpdil = 1000,
  nwells = NULL,
  nsep = 2,
  ncolmax = 105,
  dformat = "%m/%d/%Y"
)

Arguments

`antigen`	character string.
`fname`	name of the file that contains raw data.
`fdir`	directory where the file is located (alternatively, full path can be included in `fname`).
`dtype`	character string for data type in the file.
`stdstr`	character string indicating standards in the file's "Sample" column. Not case sensitive. If `""` (empty string), standards will be determined by the pattern "1/" only.
`bgstr`	character string indicating background in the file's "Sample" column. Not case sensitive.
`stddil`	a vector of standard dilutions. If `NULL`, dilutions are inferred from the file's "Sample" column. Non-null value can be used to exclude some dilutions from model fitting.
`smpdil`	single value for sample dilutions (if dilutions are not provided in `smp` data frame). Ignored if `dilvar` is provided and the variable is included in `smp` data frame.
`nwells`	number of wells. If `NULL`, inferred from the file.
`nsep`	number of lines separating different data types in the file.
`ncolmax`	maximum number of columns in the file.
`dformat`	date format in the file.