Description Usage Arguments Details Value See Also
View source: R/overlap_score_summary_vs_bin_size.R
Calculate and Summarize TopDom Overlap Scores as Function of Bin Size
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | overlap_score_summary_vs_bin_size(
dataset,
chromosomes,
bin_sizes,
rhos,
reference_rhos = rep(1/2, times = length(rhos)),
window_size = 5L,
nsamples = 50L,
weights = c("by_length", "uniform"),
domain_length = NULL,
fig_path = "figures",
fig_format = c("png", "pdf"),
xlim = NULL,
ylim_score = c(0, 1),
verbose = FALSE
)
|
dataset |
(character string) The name of the data set. |
chromosomes |
(character vector) Chromosomes to process. |
bin_sizes |
(numeric vector) The set of bin sizes (in bps) to process. |
rhos |
(numeric vector) The set of fractions (in (0,0.5]) to process. |
reference_rhos |
(numeric vector) The set of fractions (in (0,0.5]) to process. |
window_size |
(integer) The TopDom windows size.
Argument passed as |
nsamples |
(integer) Number of random samples for produce. |
weights |
(character string) A character string specifying how overlap
scores across domains should be weighted.
Argument passed as is to |
domain_length |
(optional; character string or numeric vector of length two)
If specified, controls how to filter out too short or too long TopDom domains.
Argument passed as is to |
fig_path |
If non-NULL, an image file is written to this path. |
fig_format |
Image format used for image files. |
xlim |
The range on the x axis. |
ylim_score |
The range of overlap scores on the y axis. |
verbose |
(logical) If |
Image files are written to the ‘figures/’ folder (created if missing).
A three-dimensional character array of pathname names where the
first dimension specify chromosomes
, the second bin_sizes
, and
the third 'rhos'.
Internal, overlap_score_summary_grid()
is used to calculate overlap
scores over (chromosome, bin_size, rho).
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