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.
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