makedatabase: Make customized database

In Winnie09/SCATE: SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement

Make customized database

Description

Make customized database with new bulk DNase-seq data

Usage

makedatabase(
  datapath,
  savepath,
  blacklist = NULL,
  bamfile = NULL,
  cre = NULL,
  genome = "hg19",
  genomerange = NULL
)

Arguments

datapath	path to the data package folder (e.g. myfolder/hg19/). User must first download the data package to use this function. The data package for hg19 and mm10 can be downloaded from http://jilab.biostat.jhsph.edu/projects/scate/hg19.zip or http://jilab.biostat.jhsph.edu/projects/scate/mm10.zip. The compressed file should be unzipped. If users do not want to use existing data compendium (e.g. to build a database in a new species), datapath should be set NULL, and 'genome' will be ignored.
savepath	path to save the generated database. e.g. myfolder/database.rds.
blacklist	GRanges object that identifies blacklisted regions to be filtered out.
bamfile	location of bulk DNase-seq bamfiles.
cre	dataframe of new CRE sites to be added to the database. First column: chromosome name. Second column: start position. Third column: end position.
genome	Character variable of either "hg19" or "mm10". Default is 'hg19'. Ignored when datapath is NULL.
genomerange	Data frame with two columns. First column is the chromosome and second column is the length of the genome. Only useful when datapath is NULL. Example is https://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes

Details

This function makes a new customized database if users have new bulk DNase-seq data and such information can be contribued to the model building of SCATE.

Value

a new customized database if users have new bulk DNase-seq data and such information can be contribued to the model building of SCATE.

Author(s)

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

Winnie09/SCATE documentation built on May 10, 2023, 8:10 a.m.