mgpQCMetrics: Returns genes used, removedMarkerRatios and proportion of...

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

Description

A function that returns a df of the genes used, removedMarkerRatios and proportion of variance explained by the first PC in the markerGeneProfile estimation method

Usage

mgpQCMetrics(countDf, mgpCellMarkers)

Arguments

countDf	A dataframe with a Gene row in HGNC symbols and then Subject columns.
mgpCellMarkers	A nested list with as many sub-lists of marker genes as there are for cell types

Value

Returns a dataframe with the cell type, markersUsed (list of marker genes used per cell type), removedMarkerRatios (list of removed marker ratios per cell type) and percentVariancePC1 (list of variance explained by the first PC per cell type)

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

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 and mgpCellMarkers datasets available with package

mgpQCMetricsResults <- mgpQCMetrics(countDf, mgpCellMarkers)

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