DECODER.pipeline: DECODER pipeline

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

Description

This function is used to run DECODER from bam files.

Usage

DECODER.pipeline(bulk_bam_file_path, ref = c("user", "hematopoietic",
  "pbmc", "mouse_pfc"), sc_bam_file_path = NULL, celltype.idx = NULL,
  genome = NULL)

Arguments

bulk_bam_file_path	path to bulk bam file(s)
ref	the type of reference: user/PBMC/mouse pfc/hematopoietic
sc_bam_file_path	path to single-cell bam files (only and must be required when ref=='user')
celltype.idx	ad
genome	genome assembly to be used

Value

prop	estimated proportion matrix for bulk samples

Examples

## Not run: 
prop<-DECODER.pipeline(path/to/bulk,ref='user',path/to/sc,celltype.idx,genome='hg19')

## End(Not run)

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