README.md

In ebruginski/ChromR: An R package for chromatography users

ChromR

Description

The ChromR package brings some functions to help analysts, Ph.D. students and technicians to plan and organize LC analyses. The functions are separated into 2 main sections, Pre-analysis and Post-analysis. In Pre-analysis, the functions will help to randomize the injections order, calculation of the quantity of mobile phase and the spent time of batches. The Post-analysis functions will help to organize the obtained files according to their respective batches or classes, avoiding human error.

Updates

13/10/2020 - New function to format peaklist for batch correction.

Getting Started

a) Install package dependencies

install.packages(c("devtools","lubridate", "ggplot2", "progress"))

b) Install the package

devtools::install_github("ebruginski/ChromR")

Overview

Pre-analysis functions

Sample Randomization:

x = The dataframe for this function need to have: first column as samples id and the second column as sample class.

gnumber = number of classes in the sample, need to be between 2 and 6.

gnames = names of the class, need to be the same of the input data frame.

Example:

library(ChromR)

## Input the sample list

samplelist <- read.csv("/example/samplelist.csv")

## Run the randomization function

rsamplelist <- SampleRand(x = samplelist, gnumber = 2, gnames = c("disease", "health"))

Mobile phase and time calculation:

x = path to the gradient profile .csv file, format the header as below.

runs = number of the runs.

over = overage of mobile phase to keep the system secure (%).

plot = plot the gradient profile.

Example:

library(ChromR)

gradientprof <- "/example/gradientprofile.csv"

GradCalc(x = gradientprof, runs = 15, over = 15, plot = TRUE)

Post-analysis functions

Files organizer:

x = path to the samplelist .csv file, format the header metadata as below.

filetype = extension of the files that you want to move.

by = select the type of sorting, class or batch.

remove = TRUE to remove the files from origin and FALSE to not remove.

Example:

library(ChromR)

## Set the working directory where the files are
setwd("/example")

samplelist <- "/example/samplelist.csv"

FileOrganizer(x = samplelist, filetype = ".mzML", by= "class", remove = FALSE)

ebruginski/ChromR documentation built on Feb. 3, 2023, 8:34 a.m.