preprocess {gcxgclab}

Preprocessing

Description

preprocess performs full preprocessing on a data file.

Usage

preprocess(
  filename,
  mod_t = 10,
  shift = 0,
  lambda = 20,
  gamma = 0.5,
  subtract = NULL,
  images = FALSE
)

Arguments

filename

a string object. The file name or path of the cdf file to be opened.

mod_t

a float object. The modulation time for the GCxGC sample analysis.Default is 10.

shift

a float object. The number of seconds to shift the phase by. Default is 0 to skip shifting.

lambda

a float object. A number (parameter in Whittaker smoothing), suggested between 1 to 10^5. Small lambda is very little smoothing, large lambda is very smooth. Default is lambda = 20.

gamma

a float object. Correction factor between 0 and 1. 0 results in almost no values being subtracted to the baseline, 1 results in almost everything except the peaks to be subtracted to the baseline. Default is 0.5.

subtract

a data.frame object. Data frame containing TIC data from a background sample or blank sample to be subtracted from the sample TIC data.

images

a boolean object. An optional input. If TRUE, all images of preprocessing steps will be displayed. Default is FALSE, no images will be displayed.

Details

This function performs full preprocessing on a data file. Extracts data and performs smoothing and baseline correction.

Value

A data.frame object. A list of two data frames. A TIC data frame and an MS data frame.

Examples

file <- system.file("extdata","sample1.cdf",package="gcxgclab")
frame <- preprocess(file,mod_t=.5,lambda=10,gamma=0.5,images=TRUE)