Changes in version 1.3
- lemur now automatically inserts the variables from the design
formula into the group_by argument for find_de_neighborhoods.
(thanks Katha for pushing for this feature)
- The formula parsing automatically detects global variables and adds
them to the colData. This avoids problems with the random test /
training assignment.
- Duplicate column names in colData are now longer allowed.
- Require harmony version >= 1.2.0 (thanks Maija for reporting the
problem)
Changes in version 1.1
- Make predict function faster and less memory intensive for subset
fits.
- Speed-up internal function get_groups
- Gracefully handle duplicated column names in colData(fit)
- Give better error message in test_de if cond(..) is used for a fit
that was not specified with a design formula (thanks
@MaximilianNuber for reporting)
Changes in version 1.0
- Bug fix in subsetting logic affecting predict and test_de. The
problem occured if a fit object was subsetted with indices or gene
names and the order changed, and resulted in a wrong order of the
predictions.
Changes in version 0.99.1-0.99.8
- Submission to Bioconductor, thus the jump in version number.
- Adjusted internal code to handle breaking changes in harmony v1.0.0.
- Multiple small fixes to comply with Bioconductor guidelines (see
https://github.com/Bioconductor/Contributions/issues/3152)
Changes in version 0.0.27
- Instead of include_complement, the find_de_neighborhoods function
gains a add_diff_in_diff argument. If it is true, the function
calculates the difference between the DE results inside the
neighborhood vs. outside.
- Change indices columns to neighborhood and store list of cell name
vectors in output of find_de_neighborhoods.
- Enforce unique column and row names.
Changes in version 0.0.26
- Make the neighborhoods more consistent: (1) include cells which are
connected to many cells inside the neighborhood, (2) exclude cells
from the neighborhood which are not well connected to the other
cells in the neighborhood.
- Add a control_parameters argument to find_de_neighborhoods.
- Add BiocNeighbor as a dependency.
Changes in version 0.0.25
- Detect problematic neighborhoods and skip them.
- Replace test_data_cell_size_factors by size_factor_method, which is
more flexibel. Setting size_factor_method = "ratio" uses the size
factor method described in the original DESeq paper
Changes in version 0.0.24
- Fix bug in find_de_neighborhoods that meant that accidentally
additionally zeros where included in each neighborhood pseudobulk.
The test should have more power now.
- Expose min_neighborhood_size argument in find_de_neighborhoods.
- Add test_data_cell_size_factors argument to find_de_neighborhoods
which is useful if the function is called with a subsetted fit
argument.
Changes in version 0.0.23
- Improve alignment functions: simplify algorithm, find linear
approximation to Harmony's steps, include an intercept.
- Avoid calling private methods from harmony.
- Convert character columns in colData to factors to avoid problems
when dividing data into test and training data.
- Fix bug in find_de_neighborhoods where I didn't embrace an argument.
- Remove BiocNeighbors dependency.
Changes in version 0.0.21
- Minor bug fix in find_de_neighborhoods. The function threw an error
if alignment_design != design.
- Better error messages if find_de_neighborhoods is called without
having called test_de before.
Changes in version 0.0.20
- Change defaults for find_de_neighborhoods. Increase the
ridge_penalty and add a min_neighborhood_size = 10 argument to avoid
creation of very small neighborhoods.
Changes in version 0.0.19
- Add new test_fraction argument to lemur() function. It automatically
defines a hold-out datasets for the fitting step. These hold-out
data is used to infer the differential expression of the
neighborhoods in find_de_neighborhoods. This change addresses the
double-dipping problem, where it was previously left to the user to
provide an independent matrix for the find_de_neighborhoods
function.
- As a consequence of these changes, the structure of lemur_fit
objects has changed. They gain three new fields called
fit$test_data, fit$training_data, and fit$is_test_data.
- The order and names of the arguments for find_de_neighborhoods has
changed.
Changes in version 0.0.18
- Remove alignment_method field from lemur_fit objects as it was not
used for anything.
Changes in version 0.0.17
- Rename argument name for align_by_template from alignment_template
to template
- Tweak algorithm for alignment to take cluster sizes into account
during optimization
Changes in version 0.0.13
- Change in the alignment model. Previously, the method tried to align
cells using rotations and / or stretching, however, the method could
not represent reflections! To fix this, I now allow arbitrary linear
transformations where $R(x) = (I + sum_k x_k V_k)^{-1}$. The new
alignment is more flexible and easier to infer. The downside is the
term inside the parantheses can be singular which would lead to an
error.
- Skip iteration step: first infer centering and then infer latent
space. Previously, I iterated between these steps but that either
didn't add anything or actually degraded the results.
- Set center = FALSE in find_base_point. Centering the data before
fitting the base point caused problems and made the data look less
integrated in some cases.
- Remove ambient PCA step. This was originally conceived as an
performance optimization, however it had detrimental effects on the
inference. Since a few version it was skipped per default, so
removing it should not change the inference.
- Add linear_coefficient_estimator to give more flexibility how or if
the conditions are centered.
- Reduce the minimum_cluster_membership default to 0.001 in
align_harmony to make it more sensitive.
- Make test_global an internal function again until further more
extensive testing.
- Remove base_point argument from lemur(). It wasn't used anyways.
- Refactor find_de_neighborhoods: the function can now combine the
results of different directions, selection criteria, and pseudobulk
test (on counts or continuous values). To implement this, I changed
the names of the arguments and added parameters.
- Remove many superfluous method generics and only provide the
accession via $
- Fix documentation warnings
- Rename class from 'lemur_fit_obj' to 'lemur_fit'
- Store 'contrast' in lemur_fit after calling test_de
- Add option to fit count model in find_de_neighborhoods with edgeR