Interactive R Package for Automation of Chimerism Test Data Analysis
Rchimerism was designed to automatically select informative loci and calculate chimerism to monitor the cellular dynamics involving engraftment of donor hematopoietic stem cells (HSCs) or relapse of recipient malignant cells in HSC transplant (HSCT) patients.
Rchimerism starts by reading data from files generated by ABI GeneMapper and a user defined markers file. Through the shiny interface, the donor, recipient, and sample allele matrix can be quickly compared through interactive data tables. Overall donor integration percentages are displayed. Additionally, chimerism can be calculated from double donor cord blood transplantation. The data is available for download to help verify the integrity of the data.
To install devtools, use the following command:
install.packages("devtools")
Note: Rchimerism also uses shiny and DT packages. However, those packages will be installed if using install_github
from below.
Install the shinyFiles package with this command:
install.packages("shinyFiles")
To install the Rchimerism package all the prerequisites above need to be installed.
Using the R Console, type:
devtools::install_github("BioHPC/Rchimerism")
In order to use Rchimerism, it must be loaded into the library
library(Rchimerism)
In order to use Rchimerism the data needs to be in a specific format. The locus marker input file must be in '.csv' format. The loci must be listed in the first row of the file. The donor, recipient, and sample data should be generated by the ABI GeneMapper and retain the same format.
The downloadable "Data_examples" zipped folder contains example donor, recipient, and sample data text files.
Rchimerism()
The Directory mode is intended for "power users," or technicians/clinicians tackling a large amount of data. Directory mode assumes a strict file structure (which would need to be set up) in order to speed up data entry. An example directory is included in the "Directory_example" folder. The initial use after starting the program will take the longest (file menu starts at the hard drive level, longer to navigate), but subsequent inputs will be quick due to the program remembering the previously selected files.
The Directory structure is as follows:
Example:
patientID
|___>ddata.txt
|___>rdata.txt
|___>Date
|___>cd3
| |___>sdata.txt
|___>cd33
|___>sdata.txt
Rchimerism depends on selection of the folder with "sdata.txt", and assumes that the donor and recipient files are located 2 directories above. This allows for flexibility with folder (not file) names along with additional sample types (cd3, cd33, ...)
Data files (output files from the ABI machine) should always be named as follows (strict):
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