buildSignatureMatrixUsingSeruat: Builds a signature matrix from single-cell data by calling...

In PelzKo/dwls: Dampened Weighted Least Square for Deconvolution of Bulk mRNA Data

Description

Given a single-cell matrix and cell type ids, the function constructs a gene by cell type matrix containing averaged expression values for each cell type, for highly differentially expressed genes. Differential expression analysis is conducted through Seurat.

Usage

    buildSignatureMatrixUsingSeurat(scdata, id, path, diff.cutoff=0.5, pval.cutoff=0.01)

Arguments

scdata	Gene by cell single-cell data matrix.
id	List containing cell type ids corresponding to each column of the scdata
path	String corresponding to path in which to save DE information.
diff.cutoff	Scalar corresponding to the log fold change cutoff to use when picking differentially expressed genes (default=0.5)
pval.cutoff	Scalar corresponding to the pvalue cutoff to use when picking differentially expressed genes (default=0.01)

Value

Gene by cell type matrix containing the gene expression signature of each cell type.

Examples

    buildSignatureMatrixUsingSeurat(scdata, id, path, diff.cutoff=0.5, pval.cutoff=0.01)

PelzKo/dwls documentation built on Dec. 18, 2021, 6:46 a.m.