calcAndCompare: Calculates and compares the estimations of cell types derived...

In meconsens/CellTyPETool: Facilitates Deconvolution of Bulk Tissue RNAseq Data for Disease Phenotype Analysis

Description

A function that calculates cell type proportions using two validated methods, markerGeneProfile and findCells, and then compares the cell type proportions calculated by each

Usage

calcAndCompare(countDf, mgpCellMarkers, bretCellMarkers)

Arguments

countDf	A dataframe with Gene rows and Subject columns.
mgpCellMarkers	A nested A nested list with as many sub-lists of marker genes as there are for cell types
bretCellMarkers	A dataframe with two columns, markers and cell where markers are genes for cell types and cell indicates the cell type markers are the gene for.

Value

Returns a nested list with cell type proportions calculated by the markerGeneProfile method and the BRETIGEA method and a correlation plot to compare the two

References

H. Wickham. Reshaping data with the reshape package. Journal of Statistical Software, 21(12), 2007.

H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016.

Kirill Müller and Hadley Wickham (2020). tibble: Simple Data Frames. R package version 3.0.3. https://CRAN.R-project.org/package=tibble

Mancarci, B. O., Toker, L., Tripathy, S. J., Li, B., Rocco, B., Sibille, E., & Pavlidis, P. (2017). CrossLaboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data. eNeuro, 4(6), ENEURO.0212-17.2017. https://doi.org/10.1523/ENEURO.0212-17.201

McKenzie, A.T., Wang, M., Hauberg, M.E. et al. Brain Cell Type Specific Gene Expression and Coexpression Network Architectures. Sci Rep 8, 8868 (2018). https://doi.org/10.1038/s41598-018-27293-5

R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

Wickham et al., (2019). Welcome to the tidyverse. Journal of Open Source Software, 4(43), 1686, https://doi.org/10.21105/joss.01686

Examples

# Examples 1:
# Using countDf, bretCellMarkers, mgpCellMarkers datasets available with package

calcAndCompareResults <- calcAndCompare (
                countDf = countDf,
                mgpCellMarkers = mgpCellMarkers,
                bretCellMarkers = bretCellMarkers)

meconsens/CellTyPETool documentation built on Jan. 1, 2021, 9:25 a.m.