PACMOSData

Overview

PACMOSData is an ExperimentHub data package providing reference datasets for PACMOS analyses of MESOMICS and lungNENomics cohorts.

The package contains metadata and access utilities for:

  • MESOMICS reference datasets
  • lungNENomics reference datasets
  • PACMOS example and test datasets

These datasets are intended to support reproducible multi-omics analyses using the PACMOS framework.

Installation

BiocManager::install("PACMOSData")

Load package

library(PACMOSData)

Available datasets

MESOMICS datasets

The following datasets are available for MESOMICS analyses:

  • archetypes : Archetype proportions.
  • D_alt_MOFA : Genomic Alterations.
  • D_cnv_MOFA : Copy Number Alterations.
  • D_exprB_MOFA : Gene expression data.
  • D_loh_MOFA : Loss of heterozygosity.
  • D_met.bodB_MOFA : Methylation gene body regions.
  • D_met.enhB_MOFA : Methylation enhancer regions.
  • D_met.proB_MOFA : Methylation promoter regions.
  • MESOMICS_latent_factors : MOFA latent factors.

lungNENomics datasets

The following datasets are available for lungNENomics analyses:

  • Inputs_MOFA : MOFA input matrices.
  • lungNEN_LF_K4_with_label : Archetype proportions with discrete molecular group classifications.
  • lungNEN_LF_K4_without_label : Archetype proportions without discrete molecular group classifications.
  • lungNEN_LFs : MOFA latent factors.
  • lungNEN_sample_label : Sample IDs with molecular groups.

Test datasets

The package also contains small example datasets used for testing and demonstrating PACMOS workflows:

  • lungNEN_test_expr : Test expression data for lungNENomics cohort.
  • MESOMICS_test_expr : Test expression data for MESOMICS cohort.

Data access

Data resources can be loaded using:

library(PACMOSData)

mesomics_data <- load_pacmos_data("MESOMICS")

lungnen_data <- load_pacmos_data("lungNENomics")

test_data <- load_pacmos_data("test")