fischuu/fluidigm

Fluidigm data analysis r-package

Fluidigm

Fluidigm is an R package that can analyze genotyping data from Fluidigm instruments. It can perform various operations such as:

• Converting the raw data into PLINK format
• Estimating genotyping errors
• Calculating pairwise similarities
• Determining pairwise similarity loci
• Generating a similarity matrix

Fluidigm provides a convenient interface to the powerful capabilities of the PLINK software, which is a free, open-source whole genome association analysis toolset. It also provides detailed output files and plots to help you explore and understand your genotypic data.

Installation

You can install Fluidigm from CRAN with (soon...):

install.packages("Fluidigm")

Or you can install the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("fischuu/Fluidigm")

Further requirements

Please note, that you need to have Plink installed on your system and it needs to be available on the PATH variable.

On the Plink wegpage there are aleady precompiled binaries that can be downloaded, see here

Plink 1.9 : https://www.cog-genomics.org/plink/

Plink 1.07 : https://zzz.bwh.harvard.edu/plink/download.shtml

Running example

# Load the library
  library("Fluidigm")
  
# Set the working directory
  setwd("~/Project/My_fluidigm_project")

# Define the required files
  file <- "Run.csv"
  map <- "Run.map"
  db <- "Run.ped"
  neg_controls=c("STA-blank", "Chipblank")
  
# Define y and x markers
  y.marker <- "markerY1"
  x.marker <- c("markerX1",
                "markerX2",
                "markerX3",
                "markerX4",
                "markerX5",
                "markerX6",
                "markerX7",
                "markerX8",
                "markerX9")

# Run the analysis
  out <- fluidigmAnalysisWrapper(file=file,
                                 db=db,
                                 map=map,
                                 neg_controls=neg_controls,
                                 y.marker = y.marker,
                                 x.marker = x.marker)
  
# You can also run the individual steps  

fluidigm2PLINK(...)
estimateErrors(...)
calculatePairwiseSimilarities(...)
getPairwiseSimilarityLoci(...)
similarityMatrix(...)

License

Fluidigm is licensed under the GPL-3 license. See the LICENSE file for more information.

Citation

If you use Fluidigm in your research, please cite it as follows:

citation("Fluidigm")

Contact If you have any questions, suggestions, or feedback, please feel free to contact me. I would love to hear from you and improve the package. 🙌

Acknowledgements

The package uses also a perl script that was written by Doug Scofield and which is published here:

https://github.com/douglasgscofield/bioinfo/blob/main/scripts/plink-pairwise-loci.pl