analyzeBiosensorData: Process Raw Biosensor Data

In BaileyLabUM/biosensor: Analyzes raw data from biosensors, specifically, the Maverick M1 detection system from Genalyte, Inc

Description

The purpose of this program is to process with the raw data from the Maverick M1 detection system (Genalyte, Inc., San Diego, CA) and output simple line graphs, bar charts, and box plots. In principle, this code should also work for any bionsensor data that ouputs Time in column one and Signal in column two. The function call also generates companion csv files containning processed the prcoessed data for subsequent analysis. The folder containing output from the M1 typically consists of: 1. a csv file for each ring and 2. a comments file the describes the experimental run A "comments.csv" file is also exported, but it is not needed. In addition to the csv files for each ring, a separate file containing the chip layout is required. An example of a chip layout file is provided in the "BaileyLabMRRs" repository located at https://github.com/BaileyLabUM/BaileyLabMRRs. See the "groupNames_allClusters.csv" file for an example.

Usage

analyzeBiosensorData(time1 = 51, time2 = 39,
  filename = "groupNames_XPP.csv", loc = "plots", cntl = "thermal",
  chopRun = 0, fsr = FALSE, chkRings = FALSE, plotData = TRUE,
  celebrate = FALSE, netShifts = TRUE, getLayoutFile = FALSE,
  uchannel = FALSE, mulitNet = FALSE)

Arguments

time1	a number specifying the later time for net shift calculations
time2	a number specifying the earlier time for net shift calculations
filename	a string with the filename containing the chip layout
loc	a string with directory name to save plots and data files
cntl	a string indicating the target to be used for control; the default value is "thermal"; use "raw" if you do not want to use a control
chopRun	the numerical value on where to start the run, and the data will only be "chopped" (subsetted) if 'chopRun' > 0
fsr	a logical value indicating whether the data contains FSR shifts
chkRings	a logical value indicating if rings should be removed
plotData	a logical value indicating if data should be plotted, which will save a series of png files
celebrate	a logical value, set it to TRUE for to be alerted when your script has finished
netShifts	a logical value indicating if net shift values should be calculated and plotted
getLayoutFile	a logical value indicating if the chip layout file should be downloaded from Github
uchannel	a logical value indicating if experiment is a U-channel
multiNet	a logical value indicating if there mulitple net shifts for a single run

Value

This function returns csv files containing processed data along with a number of png files containing plots of the processed data.

Examples

dir <- system.file("extdata", "20171112_gaskTestData_MRR",
                   package = "biosensor")
setwd(dir)
analyzeBiosensorData()

BaileyLabUM/biosensor documentation built on May 28, 2019, 11:36 a.m.