View source: R/SCATEpipeline.R
SCATEpipeline | R Documentation |
SCATE pipeline of reading in bam, clustering cell, and performing SCATE
SCATEpipeline(
bamfile,
genome = "hg19",
cellclunum = NULL,
CREclunum = NULL,
datapath = NULL,
ncores = 1,
perplexity = 30,
example = FALSE
)
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. |
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, Wenpin Hou, Hongkai Ji* <whou10@jhu.edu>
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)
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