CSCD | R Documentation |
Provides accurate cell-type proportion estimation by incorporating covariance structure
in given single-cell RNA-seq (scRNA-seq) and bulk RNA-seq datasets, see Karimnezhad (2022). The approach uses an extension
of the transformation used in Jew et al. (2020) implemented in the BisqueRNA::ReferenceBasedDecomposition()
function.
CSCD(
bulk.eset,
sc.eset,
min.p = NULL,
markers = NULL,
cell.types = "cellType",
subj.names = "SubjectName",
verbose = TRUE
)
bulk.eset |
ExpressionSet with bulk data. Bulk RNA-seq data can be converted from a matrix with samples in columns and genes in rows to an ExpressionSet. See |
sc.eset |
ExpressionSet with single-cell data. Single-cell data requires additional information in the ExpressionSet, specifically cell-type labels and individual labels. See |
min.p |
A percentage. This parameter is passed to the |
markers |
A character vector containing marker genes to be used in decomposition. If NULL provided, the method will use all available genes for decomposition. |
cell.types |
Character string. A vector of cell-type labels. |
subj.names |
Character string. A vector of individual labels that correspond to cells. |
verbose |
Boolean. Whether to print log info during decomposition. Errors will be printed regardless. |
A list. Slot bulk.props contains a matrix of cell-type proportion estimates with cell types as rows and individuals as columns. Slot sc.props contains a matrix of cell-type proportions estimated directly from counting single-cell data. Slot transformed.bulk contains the covariance-based transformed bulk expression used for decomposition. These values are generated by applying a linear transformation to the CPM expression. Slot genes.used contains a vector of genes used in decomposition. Slot rnorm contains Euclidean norm of the residuals for each individual's proportion estimates.
Butler, A. et al. (2019). Seurat: Tools for Single Cell Genomics. R package version, 4.1.1.
Jew, B. et al. (2020) Accurate estimation of cell composition in bulk expression through robust integration of single-cell information. Nat Commun 11, 1971. https://doi.org/10.1038/s41467-020-15816-6
Jew, B. and Alvarez, M. (2020). BisqueRNA: Decomposition of Bulk Expression with Single-Cell Sequencing. R package version, 1.0.5.
Karimnezhad, A. (2022) More accurate estimation of cell composition in bulk expression through robust integration of single-cell information. Bioinformatics Advances, Volume 2, Issue 1, 2022, vbac049. https://doi.org/10.1093/bioadv/vbac049
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