cellTypeAssign

correlation matrix between CDSeq-estimated GEPs and reference GEPs.

corMat

only the correlations that are above threshold will be considered.

threshold

Assign cell types using correlation matrix computed using cell-type-specific GEPs and reference GEPs.
<code>cellTypeAssign</code> assigns CDSeq-identified cell types to reference profile.

Estimate cell-type-specific gene expression profiles and sample-specific cell-type proportions simultaneously using bulk sequencing data. Kang et al. (2019) <doi:10.1371/journal.pcbi.1007510>.

Kai Kang

CDSeq

A Complete Deconvolution Method using Sequencing Data

Caizhi Huang

Qian Meng

Igor Shats

Melissa Li

David Umbach

Leping Li

Yuanyuan Li

Xiaoling Li

cellTypeAssign function

Assign cell types using correlation matrix computed using cell-type-specific GEPs and reference GEPs.
<code>cellTypeAssign</code> assigns CDSeq-identified cell types to reference profile. — cellTypeAssign

Assign cell types using correlation matrix computed using cell-type-specific GEPs and reference GEPs.
<code>cellTypeAssign</code> assigns CDSeq-identified cell types to reference profile.

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.

Description

Usage

Arguments

Value