genesUsed: Returns genes used in Marker Gene Profile and BRETIGEA method

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

Description

A function that returns the genes used in the markerGeneProfile estimation method and the BRETIGEA method

Usage

genesUsed(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 mgpMarkers and bretMarkers which are each lists of markers used for each method

References

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

Stefan Milton Bache and Hadley Wickham (2014). magrittr: A Forward-Pipe Operator for R. R package version 1.5. https://CRAN.R-project.org/package=magrittr

Examples

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

genesUsedResults <- genesUsed (
                countDf = countDf,
                mgpCellMarkers = mgpCellMarkers,
                bretCellMarkers = bretCellMarkers)

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