A Complete Deconvolution Method using Sequencing Data


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Documentation for package ‘CDSeq’ version 1.0.8

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CDSeq-R-package CDSeq: A package for complete deconvolution using sequencing data
CDSeq Complete deconvolution using sequencing data.
cdseq.result Output of synthetic mixtures of PBMC scRNAseq data
Cell2RNA Cell proportion to RNA proportion 'Cell2RNA' converts Cell proportion to RNA proportion
cellTypeAssign Assign cell types using correlation matrix computed using cell-type-specific GEPs and reference GEPs. 'cellTypeAssign' assigns CDSeq-identified cell types to reference profile.
cellTypeAssignMarkerGenes 'cellTypeAssignMarkerGenes' assigns CDSeq-identified cell types using user-provided marker gene list and plots heatmap.
cellTypeAssignSCRNA 'cellTypeAssignSCRNA' assigns CDSeq-identified cell types using single cell RNAseq data.
gene2rpkm gene2rpkm outputs the rpkm normalizations of the CDSeq-estimated GEPs. 'gene2rpkm' outputs the rpkm normalizations of the CDSeq-estimated GEPs.
gene_length Gene length
gibbsSampler This is the Gibbs sampler for CDSeq. 'GibbsSampler' returns estimated GEPs and cell type proportions.
hungarian_Rcpp This is the Hungarian algorithm wrapper for cell type assignment 'hungarian_Rcpp' returns cell type assignment given reference GEPs
intersection 'intersection' take intersection of multiple lists and return the common set and index
logpost logpost computes the log posterior of the CDSeq model. 'logpost' outputs the value of log posterior.
max_rep 'max_rep' Find the element that repeats the most in a given vector and calculate its proportion.
merge_df Data frame for keeping the CDSeq-estimated cell type proportions for PBMC mixtures
mixtureGEP Synthetic bulk RNA-seq read counts data of six cell types
pbmc_ggplot ggplot figures of comparison between CDSeq-estimated cell type proportion and ground truth
pbmc_mix Synthetic bulk RNA-seq read counts data of PBMC single cell data
read2gene read2gene outputs the GEP normalized by gene length of the CDSeq-estimated GEPs. 'read2gene' outputs the gene length normalized CDSeq-estimated GEP.
refGEP GEPs of six component pure cell lines
result1 CDSeq result of synthetic bulk RNA-seq read counts data of six cell types
result2 CDSeq result of synthetic bulk RNA-seq read counts data of six cell types
result3 CDSeq result of synthetic bulk RNA-seq read counts data of six cell types
RNA2Cell RNA proportion to cell proportion 'RNA2Cell' converts RNA proportion to cell proportion
sc_annotation Cell type annotation of the PBMC single cell data
sc_gep PBMC single cell RNAseq read counts that used for creating synthetic PBMC mixtures
seedMT This is the Mersenne Twister random number generator. 'cokus' generates pseudorandom integers uniformly distributed in 0..(2^32 - 1).
SyntheticMixtureData Synthetic bulk RNA-seq read counts data of six cell types, PBMC mixtures using scRNASeq and some preliminary results
true_GEP_gene True GEPs of the six component cell types normalized by gene length
true_GEP_read True GEPs of the six component cell types unnormalized by gene length
true_GEP_rpkm True GEPs of the six component cell types RPKM normalization
true_prop True cell type proportion in the PBMC synthetic mixtures
true_prop_cell True cell proportions of the mixtures
true_prop_RNA True cell type RNA proportions