# A Complete Deconvolution Method using Sequencing Data

## Documentation for package ‘CDSeq’ version 1.0.9

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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
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