Package 'SIPETool'

Title: SIFT-MS and CPET Data Processor
Description: Processor for selected ion flow tube mass spectrometer (SIFT-MS) output file from breath analysis. It allows the filtering of the SIFT output file (i.e., variation over time of the target analyte concentration) and the following analysis for the determination of: maximum, average, and standard deviation value of target concentration measured at each exhalation, and the respiratory rate over the measurement. Additionally, it is possible to align the SIFT-MS data with other on-line techniques such as cardio pulmonary exercise test (CPET) for a comprehensive characterization of breath samples.
Authors: Federico Vivaldi; Tommaso Lomonaco
Maintainer: Federico Vivaldi <[email protected]>
License: GPL-3
Version: 0.1.0
Built: 2025-03-12 03:13:04 UTC
Source: https://github.com/cran/SIPETool

Help Index

SIPETool example files

Description

Raw and filtered output from SIFT-MS, and CPET system. Four different files are available: raw_sift -> raw data from SIFT-MS CPET_time -> data from CPET system for time allignment SIFT_time -> filtered data from SIFT-MS for time allignment SIFT_filtered -> raw data from SIFT-MS filtered using SIFT_output_filter

data indexer

Description

This function takes as input a vector and return the data index according to the selected time frame

Usage

data_indexer(dat, time_frame_index = NA)

Arguments

dat

input vector
time_frame_index

custom data range from the time column

Value

a vector indexed according to the specified time frame

Examples

data_indexer(c(1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1))

Data normalizer

Description

This function takes as input a vector and returns it normalized between a specified range

Usage

normalizer(dat, norm_range = c(0, 1))

Arguments

dat

the vector to normalize
norm_range

the range used for normalization

Value

vector normalized between norm_range

Examples

normalizer(c(1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1))

SIPETool example files

Description

Raw and filtered output from SIFT-MS, and CPET system. Four different files are available: raw_SIFT -> raw data from SIFT-MS CPET_time -> data from CPET system for time allignment SIFT_time -> filtered data from SIFT-MS for time allignment SIFT_filtered -> raw data from SIFT-MS filtered using SIFT_output_filter

SIPETool example files

Description

Raw and filtered output from SIFT-MS, and CPET system. Four different files are available: raw_sift -> raw data from SIFT-MS CPET_time -> data from CPET system for time allignment SIFT_time -> filtered data from SIFT-MS for time allignment SIFT_filtered -> raw data from SIFT-MS filtered using SIFT_output_filter

SIFT output filter

Description

This function takes as input the output file generated by the SIFT-MS and returns a .csv containing the TIME and the concentrations data selected by the user

Usage

SIFT_output_filter(
  setdir = getwd(),
  input_name = file.choose(),
  output_name,
  n_parameters = 2,
  param_names = c("Isoprene", "Acetone"),
  out_file = TRUE
)

Arguments

setdir

allow the selection of the working directory
input_name

allow the selection of the input file
output_name

name of the .csv output file
n_parameters

number of analytes
param_names

vector with name of the analytes
out_file

flag for the export of a csv file

Value

Filtered data and optional csv from SIFT input

Examples

data(raw_SIFT)
SIFT_output_filter(input_name = raw_SIFT, output_name = "testfile", out_file = FALSE)

SIPETool example files

Description

Raw and filtered output from SIFT-MS, and CPET system. Four different files are available: raw_sift -> raw data from SIFT-MS CPET_time -> data from CPET system for time allignment SIFT_time -> filtered data from SIFT-MS for time allignment SIFT_filtered -> raw data from SIFT-MS filtered using SIFT_output_filter

Sign detection

Description

This function takes as input a vector and returns the sign of each element

Usage

sign_detect(dat)

Arguments

dat

the vector to be used

Value

vector with the signs of each element of the original matrix

Examples

sign_detect(c(1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1))

Tidal analyzer

Description

This function takes as input a csv file containing a time column and data columns and returns the position of the end tidals for each data column maximazing the syncronization between data. This function was originally devised for the analysis of the end tidals coming from exhaled breath analyzed through SIFT-MS technology

Usage

tidal_analyzer(
  setdir = getwd(),
  input_name = file.choose(),
  output_name,
  starting_threshold = 0.03,
  time_frame = NA,
  out_file = TRUE
)

Arguments

setdir

working directory
input_name

csv file
output_name

name of the output file
starting_threshold

initial value for the dynamic threshold
time_frame

custom data range from the time column
out_file

flag for the export of a csv file

Value

csv containing the end tidals, their maximum, average, frequency, and timing

Examples

data(SIFT_filtered)
tidal_analyzer(input_name = head(SIFT_filtered, n = 100), output_name = "out", out_file = FALSE)

Tidal finder

Description

This function takes as input a matrix and returns for each column the end tidals depending of the threshold set. It is possible to set a custom time frame for the search of the tidals. Note: a minimum amount of 45 points are necessary.

Usage

tidal_finder(
  dat,
  height_threshold = 0.2,
  refine = FALSE,
  time_frame_index = NA
)

Arguments

dat

the input matrix
height_threshold

the minimum height of the tidal
refine

refine the dataset
time_frame_index

custom time frame

Value

matrix with the tidals for each column

Examples

tidal_finder(c(1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1))

Time_alignment

Description

This function takes as input two data set containing a time vector and a data vector and return the two data sets aligned. This is done by reducing the dimensions of the data set with higher points. The first data set is the one coming from the CPET-ESE and the second one from the SIFT-MS

Usage

time_filter(Cy = file.choose(), sift = file.choose())

Arguments

Cy

CPET-ESE output file
sift

SIFT-MS refined file

Value

A plot and the SIFT-MS data file resized for the alignment with the CPET-ESE file

Examples

data(SIFT_time)
data(CPET_time)
time_filter(CPET_time, SIFT_time)

Trend finder

Description

This function takes as input a vector and returns the trend of each column expressed as the difference between two consecutive elements

Usage

trend(dat)

Arguments

dat

the vector to analyze

Value

vector containing the trend of the each column

Examples

trend(c(1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1))