PACMOSData

PACMOSData is an ExperimentHub data package providing reference datasets required for running the PACMOS framework on MESOMICS and lungNENomics cohorts.

The package contains metadata and access utilities for:

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

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Installation

if (!requireNamespace("remotes", quietly = TRUE)) {
    install.packages("remotes")
}

remotes::install_github("lipikakalson/PACMOSData")

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Usage

library(PACMOSData)

mesomics_data <- load_pacmos_data("MESOMICS")

lungnen_data <- load_pacmos_data("lungNENomics")

test_data <- load_pacmos_data("test")

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Available datasets

MESOMICS

1. archetypes : Archetype proportions.
2. D_alt_MOFA : Genomic Alterations.
3. D_cnv_MOFA : Copy Number Alterations.
4. D_exprB_MOFA : Gene expression data.
5. D_loh_MOFA : Loss Of Heterogeneity.
6. D_met.bodB_MOFA : Methylation gene body regions.
7. D_met.enhB_MOFA : Methylation enhancer regions.
8. D_met.proB_MOFA : Methylation promoter regions.
9. MESOMICS_latent_factors : MOFA latent factors.

lungNENomics

1. Inputs_MOFA : MOFA input matrices.
2. lungNEN_LF_K4_with_label : Archetype proportions with discrete molecular group classifications.
3. lungNEN_LF_K4_without_label : Archetype proportions without discrete molecular group classifications.
4. lungNEN_LFs : MOFA latent factors.
5. lungNEN_sample_label : Sample IDs with molecular groups.

Test datasets

1. lungNEN_test_expr : Test expression data for lungNENomics cohort.
2. MESOMICS_test_expr : Test expression data for MESOMICS cohort.

Related package

Main software package:

• PACMOS

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