Description Usage Arguments Details Value Author(s)
Make customized database with new bulk DNase-seq data
1 2 3 4 5 6 7 8 9 | makedatabase(
datapath,
savepath,
blacklist = NULL,
bamfile = NULL,
cre = NULL,
genome = "hg19",
genomerange = NULL
)
|
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 |
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.
a new customized database if users have new bulk DNase-seq data and such information can be contribued to the model building of SCATE.
Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji* <whou10@jhu.edu>
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