DraculR R package

A small repository for the DraculR minimun working code

DraculR is a new lightweight tool for haemolysis detection in human plasma miR-Seq datasets. See original publication and github repository here

The original code allow you to execute a DraculR Shiny.io page here or using a local version

What is the difference here?

Here, we have just set the code for the calculation of the draculR haemolysis score so that given a dataframe of miRNA counts, it determines the haemolysis score.

No plots neither distributions are plotted. Please refer to the original code or shiny app to do so.

Please refer and cite the original code/paper appropriately.

Smith, Melanie D., Shalem Y. Leemaqz, Tanja Jankovic-Karasoulos, Dale McAninch, Dylan McCullough, James Breen, Claire T. Roberts, and Katherine A. Pillman. 2022. “Haemolysis Detection in MicroRNA-Seq from Clinical Plasma Samples.” Genes 13 (7). https://doi.org/10.3390/genes13071288.

How to use it

Please ensure the following packages are installed on your local machine:

library(dplyr)
library(plyr)
library(tidyr)
library(magrittr)
library(edgeR)

To install the draculR.HCGB package you can either clone the repository and source the functions or install the developer R package

Clone and source

  $ cd folder/to/clone-into/
  $ git clone https://github.com/HCGB-IGTP/draculR.HCGB/
  $ cd draculR.HCGB
  $ source R/draculR_validate.R
  $ source R/draculR_counts.R

Install R package

# Install version from GitHub:
install.packages("devtools")
devtools::install_github("HCGB-IGTP/draculR.HCGB")

Usage example

We will be using the original example provided by draculR developers available in dataExample/ folder.

The format is either csv or tsv and contains:

• raw counts of miRNAs for each sample
• sample names as column names
• the first column must be named "mir_name" and contains miRNAs names, following mirBase convention. See details here

See an example here:

mir_name	sample1	sample2	sample3
hsa-let-7a-5p	34884	29245	31451
hsa-let-7e-5p	721	354	326
hsa-let-7f-1-3p	2	0	1
hsa-miR-1-3p	50	16	65
hsa-miR-100-5p	6	9	6
hsa-miR-101-3p	964	2021	2287
hsa-miR-101-5p	1	1	0
hsa-miR-103a-3p	5090	2728	2994
hsa-miR-106a-5p	2	4	1
hsa-miR-107	160	319	256
hsa-miR-10a-3p	2	2	0

You can now open the example_code.R script and execute it from RStudio to get a working example.

See the code here:

test_file <- "./dataExample/exampleCounts.csv"
counts.test <- draculR.HCGB::draculR_parse_file(raw_data = test_file, sep_input = ",", verbose = FALSE)
draculR_results <- draculR.HCGB::draculR_parse_counts(counts_df = counts.test)
draculR_results