Description Usage Arguments Value Parallel processing Examples
View source: R/topdom_partitions.R
Fit TopDom Across Partitions
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
reads |
A base::data.frame. |
bin_size |
A positive numeric. |
partition_by |
A string specifying how to partition;
one of |
rho, reference_rho |
A numeric in (0,1/2] specifying the relative size of the partitions. |
nsamples |
Number of random samples. |
seed |
Random seed for reproducible (parallel) random number generation (RNG). |
chrs |
(optional, filter) Names of chromosomes to iterate over.
Defaults to the chromosomes in |
min_cell_size |
(optional, filter) The minimum number of reads for a cell to be included. Cells with less reads are dropped. |
dataset |
(optional) ... |
cell_ids |
(optional, filter) ... |
window_size |
A positive integer passed to TopDom::TopDom.
Defaults to |
path_out |
The root folder where to write output. |
mainseed |
... |
force |
If |
as |
Should values or pathnames be returned? |
verbose |
If |
A named list of length length(chrs)
with names as chrs
.
Each list elements contains nsamples
pathnames of RDS files.
The future framework is used to parallelize TopDom::TopDom in three layers:
across chromosomes (argument chrs
)
across random samples (argument nsamples
)
per random sample, across partitions (argument partition_by
)
typically two ('reference' and one more)
1 2 3 4 5 6 7 8 | dataset <- "human,HAP1,unique"
pathname <- system.file("compiledData", sprintf("%s,chr=22.rds", dataset), package = "TopDomStudy")
reads <- read_rds(pathname)
print(reads)
td <- topdom_partitions(reads, bin_size = 100e3, rho = 0.5, nsamples = 5L,
partition_by = "cells_by_half",
dataset = dataset, verbose = TRUE)
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