SCATEpipeline: SCATE Pipeline

In SCATE: SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement

Description

SCATE pipeline of reading in bam, clustering cell, and performing SCATE

Usage

SCATEpipeline(
  bamfile,
  genome = "hg19",
  cellclunum = NULL,
  CREclunum = NULL,
  datapath = NULL,
  ncores = 1,
  perplexity = 30,
  example = FALSE
)

Arguments

bamfile	Character vector of bam files to be processed
genome	Character variable of either "hg19" or "mm10".
cellclunum	Numeric variable giving the number of cell clusters when clustering cells. If NULL the cluster number will be determined automatically.
CREclunum	Numeric variable giving the number of CRE clusters when running SCATE. If NULL the cluster number will be determined automatically.
datapath	Character variable of the path to the customized database (eg myfolder/database.rds). The database can be made using 'makedatabase' function. If not null, 'genome' is ignored.
ncores	Numeric variable of number of cores to use. If NULL, the maximum number of cores is used.
perplexity	Numeric variable specifying perplexity of tSNE. Reduce perplexity when sample size is small.
example	An indicator of whether this is running an example or real data. When running a real data, this should be set as FALSE. The default is FALSE.

Details

This function takes as input a list of bam files. It then read in the bam files, cluster cells, and performs SCATE for each cell cluster

Value

A list of three elements. First element is a list generated by cellcluster function, and it contains the cell clustering results. Second element is a matrix generated by SCATE function. Each column is the SCATE result for one cell cluster. Column names indicate the cluster id. Third element is a list of peaks. Each element is the peak list for one cluster. Name of the element indicates the name of the cluster.

Author(s)

Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji* <[e-mail]>

Examples

f <- list.files(paste0(system.file(package="SCATEData"),"/extdata/"),full.names = TRUE,pattern='.bam$')
#Users need to set CREclunum to be NULL in real applications.
SCATEpipeline(f[1],genome="hg19",CREclunum=156,perplexity=0.1,example=TRUE) 

SCATE documentation built on Nov. 8, 2020, 5:56 p.m.