CBS_PBMC_array: An example dataset for partial reference-free cell...
In ziyili20/TOAST: Tools for the analysis of heterogeneous tissues
CBS_PBMC_array R Documentation
An example dataset for partial reference-free
cell composition estimation from tissue gene expression
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$prior_sigma
ziyili20/TOAST documentation built on Aug. 28, 2022, 11:28 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| CBS_PBMC_array | R Documentation |
An example dataset for partial reference-free cell composition estimation from tissue gene expression
Description
The dataset contains 511 microarray gene expressions for 20 PBMC samples (mixed_all) and PBMC microarray reference for the matched 511 genes from 5immune cell types (LM_5). It also contains the true cell compositions from cell sorting experiment (trueProp) and prior knowledge of cell compositions for 5 cell types in PBMC (prior_alpha and prior_sigma).
Usage
data("CBS_PBMC_array")
References
Newman, Aaron M., et al. "Robust enumeration of cell subsets from tissue expression profiles." Nature methods 12.5 (2015): 453.
Rahmani, Elior, et al. "BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference." Genome biology 19.1 (2018): 141.
Examples
data("CBS_PBMC_array")
CBS_PBMC_array$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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.