SCATEpipeline: SCATE Pipeline
In zji90/SCATE: SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement

Description Usage Arguments Details Value Author(s) Examples

View source: R/SCATEpipeline.R

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

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

`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.

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

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.

Zhicheng Ji, Weiqiang Zhou, Hongkai Ji <zji4@zji4.edu>

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set.seed(12345)
f <- list.files(paste0(system.file(package="SCATE"),"/extdata/example"),full.names = TRUE)
SCATEpipeline(f,genome="hg19",CREclunum=5000,perplexity=5)