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TopDom() no longer produces a warning
object 'idxs' not found when called on data where no region
can be processed, e.g. when every non-gap run of bins is shorter than
the minimum region size.
TopDom() with statFilter = TRUE
(default) on extremely sparse data used to fail deep inside
stats::wilcox.test() with an obscure
not enough (finite) 'x' observations error. It now fails
early with an informative message explaining that the data is too sparse
for the statistical-filtering step and suggesting remedies such as
statFilter = FALSE or a larger bin size.
TopDom() with statFilter = TRUE
(default) on a very large contact matrix (more than
sqrt(.Machine$integer.max), i.e. 46340, bins) used to fail
with an obscure 'to' must be a finite number error from
seq(), preceded by an
NAs produced by integer overflow warning, because the
internal n_bins * n_bins index arithmetic overflowed R’s
integer range. It now fails early with an informative message suggesting
statFilter = FALSE or a larger bin size.
countsPerRegion(), subsetByRegion(),
readHiC(), ggCountHeatmap(),
ggDomain(), ggDomainLabel(),
legacy(), the overlapScores() methods, several
TopDom() options (statFilter,
outFile, debug, file-path input), and internal
utility functions.Fix equation format issue and update one URL.
Drop stale and redirecting URLs (dead lab-software and USC library pages, PubMed/PMC links) in the help pages and README, keeping DOIs for the cited publications.
Package now includes mouse Chr19 data from the TopDom study. They
can be found in the
system.file("exdata", package = "TopDom") folder.
The orignal TopDom scripts TopDom_v0.0.1.R and
TopDom_v0.0.2.R are now distributed part of the package
as-is. They can be found in the
system.file("original-scripts", package = "TopDom")
folder.
readHiC() gained arguments ... which is
passed as-is to read.table().
ggCountHeatmap() for TopDomData could
produce a warning on a partial argument name.overlapScores() now has column chromosome as
the first position. The data.frame:s are of kind
tibble.as_tibble() for
TopDomOverlapScores.Add further documentation on the window.size
parameter.
Add reference to Hanjun Shin’s PhD thesis.
Improved help on overlapScores() and
TopDom().
Provide a reference for the default value for
window.size of TopDom().
The TopDom object returned by TopDom() now has an
attribute parameters which records the value of arguments
window.size and statFilter.
Made TopDom() faster and more memory efficient by
lower the number of replicated computations.
TopDom() asserting that
the intermediate and final results are of proper length and does not
contain missing values.Convert.Bin.To.Domain.TMP() used by
TopDom() could produce
Error in[<-.data.frame(tmp, , "to.coord", value = c(NA, 2500, 247500 : replacement has 3 rows, data has 1,
because it assumed at least one domain was identified.overlapScores() to be in
singular form, e.g. best_score instead of
best_scores.overlapScores() returns also the lengths of the
reference domains.overlapScores() and renamed the second argument to
reference. This was done in order to make it clear which
set of topological domains the overlap scores are calculated relative
to.Add countsPerRegion() for calculating the total
contact-frequency counts per region specified, e.g. per domain.
Add print(), dim(), [(),
and subsetByRegion() for TopDom objects where the number of
rows in the dimension reflect the number of TopDom domains.
The legacy TopDom() functions, available via
legacy(), also accept TopDomData objects as
returned by readHiC(). This is supported mostly to make it
possible to efficiently compare the different implementations.
Added [() for TopDomData objects,
e.g. tdd[1:100].
Added subsetByRegion() for TopDomData
objects.
Added ggCountHeatmap(), ggDomain(), and
ggDomainLabel() for TopDomData
objects.
legacy() for access to the original TopDom
v0.0.1 and TopDom v0.0.2 implementations,
e.g. TopDom::legacy("0.0.1")$TopDom().TopDom() itself were the
ones from TopDom v0.0.2.Add overlapScores().
Add image() for TopDomData.
List returned by TopDom() gained class
TopDom.
Added logical option TopDom.debug, which controls
whether functions produce debug output or not. The default is
FALSE.
help("TopDom") with
details from the TopDom Manual (an online PDF) provided by Shin et
al.Add print() method for TopDomData
object.
Reference the TopDom paper (Shin et al., 2016) in the help and the README.
Turned the original TopDom R script into a package.
All progress messages are outputted done to standard error.
Add readHiC().
TopDom() can now read, via readHiC(), a
pure count matrix file without bin information. To read such files,
specify what chromosome is being read (argument chr) and
the bin size of the count matrix (argument
binSize).
If the matrix file is not of a known format, then
TopDom() produces an informative error. Previously it gave
a message on stdout and returned 0.
TopDom v0.0.2 script from http://zhoulab.usc.edu/TopDom/ with the below entries from the official release note:
Gap Identification module is changed.
Minor bug related to Change Points identification in very small regions is fixed.
bed format support.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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