ExampleGeneLists: Example Gene Lists
In CellMapper: Predict genes expressed selectively in specific cell types

Description Usage Details Value Author(s) References See Also Examples

Query genes, positive control genes, and negative control genes for example cell types.

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data(ExampleQueryGenes)
data(PositiveControlGenes)
data(NegativeControlGenes)

'ExampleQueryGenes' is a data frame listing the cell types and query genes analyzed in Nelms, et al. (2016). These genes can be used as query or control genes for custom CellMapper searches, and are also provided for reproducibility of the manuscript results. All predictions from the manuscript can be generated using the ReplicateManuscript function. The 'Dataset' column indicates which dataset(s) were used for each cell type, available from Bioconductor's ExperimentHub. All datasets are available from the CellMapperData package.

'PositiveControlGenes' is a list of positive control genes for each cell type used in Nelms, et al. (2016). These positive control genes were NOT provided to the algorithm, but were used to assess the accuracy of the results. This list contains Entrez gene IDs.

'NegativeControlGenes' is a list of negative control genes for each cell type used in Nelms, et al. (2016). These negative control genes were NOT provided to the algorithm, but were used to assess the accuracy of the results. This list contains Entrez gene IDs.

'ExampleQueryGenes' is a data frame, 'PositiveControlGenes' and 'NegativeControlGenes' are both lists of character vectors

Brad Nelms

B.D. Nelms, L. Waldron, L.A. Barrera, A.W. Weflen, J.A. Goettel, G. Guo, R.K. Montgomery, M.R. Neutra, D.T. Breault, S.B. Snapper, S.H. Orkin, M.L. Bulyk, C. Huttenhower and W.I. Lencer. CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. Genome Biology 2016, 17(1).

CMsearch, ReplicateManuscript, CellMapperData, ExperimentHub

1 2	data(ExampleQueryGenes) head(ExampleQueryGenes)

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Attaching package: 'BiocGenerics'

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Attaching package: 'S4Vectors'

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Warning messages:
1: replacing previous import 'stats::sd' by 'S4Vectors::sd' when loading 'CellMapper' 
2: replacing previous import 'stats::var' by 'S4Vectors::var' when loading 'CellMapper' 
           CellType GeneName EntrezID             Dataset
1        Adipocytes    FABP4     2167 EH171, EH172, EH173
2        Astrocytes  ALDH1L1    10840               EH170
3           B Cells     CD19      930 EH171, EH172, EH173
4    Cardiomyocytes    TNNI3     7137 EH171, EH172, EH173
5      Chondrocytes     ACAN      176 EH171, EH172, EH173
6 Endothelial Cells      TEK     7010 EH171, EH172, EH173