DECODER: DECODER: Deconvolution of DNA accessibility based on...

In jwyang16/DECODER: DECODER: DECOnvolution of DNA accEssibility using anchor-based Regression

Description

This function is used to deconvolve bulk ATAC-seq samples.

Usage

DECODER(bulk.dataset, ref = c("user", "hematopoietic", "pbmc",
  "mouse_pfc"), singlecell.dataset = NULL, celltype.idx = NULL)

Arguments

bulk.dataset	bulk ATAC-seq raw count matrix
ref	the type of reference: user/PBMC/mouse pfc/hematopoietic
singlecell.dataset	scATAC-seq raw count matrix. A required input when ref==user; equal to NULL when using built-in reference.
celltype.idx	cell type labels of scATAC-seq. DECODER will cluster the scATAC-seq data when equal to NULL in 'user' mode; equal to NULL when using built-in reference.

Value

prop	estimated proportion matrix for bulk samples

Examples

## Not run: 
prop<-DECODER(bulk.dataset,ref='user',singlecell.dataset,celltype.idx)

## End(Not run)

jwyang16/DECODER documentation built on Nov. 4, 2019, 3:28 p.m.