lodutilities package 🔬📊

Hi everyone 👋🏻!
In this package, you can find some useful functions and files to perform your analysis.

Installation

To install the package run devtools::install_github("mmiots9/lodutilities"). It will install the package as well as its dependencies.

Functions

Here, you can find the explanation of the various functions.

PCRAnalysis

This function allows to analyze qPCR data. In particular, it takes as input the output file (xlsx) of the analysis and returns a sheet (on the same file or on another) containing a table for each sample with these columns: target | Rep1...Repn | Mean | sd | deltaCT | foldchange

Input

The inputs of the function are:

• inputfile: String containing the name of the input file. If left NA (default), a prompt will ask you to select the file
• outputfile: String containing the name of the output file. If left NA (default), the outputfile will be the same as the inputfile (NOT overwriting it)
• max_rep_diff: Number indicating the max range between min and max CT replicate (default 0.8)
• housekeeping: Name of the housekeeping gene (default GADPH)
• sheetname: String containing the name of the new sheet (default Analysis). It should NOT exist in outputfile yet

Output

The output is an xlsx sheet, containing one table for each sample with these columns:
target | Rep1...Repn | Mean | sd | deltaCT | foldchange

deltaCT and foldchange are calculated from the housekeeping gene inserted as input. Replicates which exceed max_rep_diff are deleted and not used for calculations.