CBS_PBMC_array: An example dataset for partial reference-free cell...

In TOAST: Tools for the analysis of heterogeneous tissues

Description

The dataset contains 511 microarray gene expressions for 20 PBMC samples (mixed_all) and PBMC microarray reference for the matched 511 genes from 5immune cell types (LM_5). It also contains the true cell compositions from cell sorting experiment (trueProp) and prior knowledge of cell compositions for 5 cell types in PBMC (prior_alpha and prior_sigma).

Usage

data("CBS_PBMC_array")

References

Newman, Aaron M., et al. "Robust enumeration of cell subsets from tissue expression profiles." Nature methods 12.5 (2015): 453.

Rahmani, Elior, et al. "BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference." Genome biology 19.1 (2018): 141.

Examples

data("CBS_PBMC_array")
CBS_PBMC_array$mixed_all[1:5,1:5]
head(CBS_PBMC_array$LM_5,3)
head(CBS_PBMC_array$trueProp,3)
CBS_PBMC_array$prior_alpha
CBS_PBMC_array$prior_sigma

TOAST documentation built on Nov. 8, 2020, 5:55 p.m.