PersonalisIO

This package provides convenience functions for reading real-world evidence data provided by Personalis into Bioconductor MultiAssayExperiment objects

Basic Usage

# List of folders with Personalis data (each folder represents one sample)
sample_list = c("/tmp/personalis_example_data/sample1", "/tmp/personalis_example_data/sample2")

# Load the data
mae <- PersonalisIO::read_personalis(sample_list)

# mae is a MultiAssayExperiment with the following structure
mae
#> A MultiAssayExperiment object of 8 listed
#>  experiments with user-defined names and respective classes.
#>  Containing an ExperimentList class object of length 8:
#>  [1] gene_expression: SummarizedExperiment with 22956 rows and 5 columns
#>  [2] dna_small_variants_somatic: SummarizedExperiment with 6097 rows and 5 columns
#>  [3] dna_small_variants_tumor: SummarizedExperiment with 376654 rows and 5 columns
#>  [4] rna_small_variants_somatic: SummarizedExperiment with 5302 rows and 5 columns
#>  [5] rna_small_variants_tumor: SummarizedExperiment with 201347 rows and 5 columns
#>  [6] msi: SummarizedExperiment with 5 rows and 5 columns
#>  [7] cnv: SummarizedExperiment with 145 rows and 5 columns
#>  [8] tcr: SummarizedExperiment with 2 rows and 5 columns

For more details, see the Documentation:

• Vignette
• function reference

Installation

For now, please install the development version of the package using remotes:

install.packages("remotes")
remotes::install_github("Boehringer-Ingelheim/Personalis-io")

If there is enough interest, we will consider submitting the package to Bioconductor.

Contact

Please use the issue tracker.

Credits

This package was developed by Gregor Sturm with contributions from Christopher Mohr, Neetika Nath and Germán Leparc.