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NEWS.md

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NEWS file

IST 0.5.30

  • Fixed NAMESPACE exports for data objects
  • Added more readable default labels

IST 0.5.29

  • Fixed bug where the vignette could not be built

IST 0.5.28

  • Fixed bug where max.genes would not work for ggplot/long table format

IST 0.5.27

  • Added the max.genes option to plot genemaps -- by default it keeps all genes (so nothing changes from prior versions), but allows limiting their number

IST 0.5.26

  • Minor fixes in show methods
  • Now pathway metadata can be specified (optional), and the automatic columns mod (oc or bin) and n.genes (after mapping to human data) are added
  • Pathway metadata can be displayed in pathwaymaps by using vars.meta.path

IST 0.5.25

  • Updates in vignette, including graphical scheme
  • Updated syntax
  • Added section on pathway/sig prioritisation

IST 0.5.24

  • Added prioritisers for pathways and signatures
  • Fixed inexistent default argument in get.tab.pathwaymap
  • Legacy batch functions are skipped in unit testing

IST 0.5.23

  • Important change: group now belongs to ist.results objects, not to ist.pathways. This avoids having to fit pathways again to change the groups.
  • Error raises if id.ref or id.ist are all FALSE
  • The orthology mapping and the ensembl-symbol mapping are now accessible with :: (lazydata was not set in DESCRIPTION)
  • ist.path can be defined with empty pathway tables for oc or bin
  • Added getters for data, reponse, gene and pathway ids, sample groups and their levels

IST 0.5.22

  • Fixed bug in pheatmap with NULL title
  • Updated NAMESPACE

IST 0.5.21

  • Allowed cartesian in data.table joins, as this would raise exceptions in when going to 100k+ rows in delta tables
  • When sig.ids has no overlap with a pathway, get.tab.genemap() would raise an error - now returns NULL with a message
  • Added option of plot titles, and genemaps have the pathway name by default
  • Added helpers save.pheatmap(), save.genemaps() and save.boxplots() to provide a default way of exporting the basic plots

IST 0.5.20

  • Minor modifications so that CI goes through

IST 0.5.19

  • Fixed issue of missing gene labels in ist.results
  • Added two label mapping vectors ready to use in ist.results instead of data.frame
  • Expanded options for pheatmap through the args.pheatmap argument and its defauls
  • Added getGroups(), getMetaSig() and refactored some slot accessions
  • By default, group is ordered now

IST 0.5.18

  • Fix order issue in boxplots
  • Fixed default boxplot: now shows original data groups
  • Fixed colour scale in heatmaps

IST 0.5.17

  • Updated vignette
  • Exported plotting functions

IST 0.5.16

  • Small fixes to do.isx() (legacy) and to plot.ist.boxplot() (bug)

IST 0.5.15

  • Fixed error in default gene labels
  • Now signatures can be subsetted in every plot type with sig.ids
  • Removed assertions of strict subsets in signature/pathway ids

IST 0.5.14

  • Added default orthology mappings data.list.orth and gene labels for plotting data.dt.genelabels
  • Added the slot @vec.gene2label to ist.results; if provided, gene labels are switched in the genemaps

IST 0.5.13

  • Fixed original signature metadata, that had extra rows
  • Moved id.ist and id.ref to the ist.results object
  • Updated vignette with current signature and pathway classes
  • Updated CI dependencies

IST 0.5.12

  • Added more getters, esp getSignatures() and getPathways()
  • Added plotting functions: plot.ist.boxplots(), plot.ist.genemaps(), plot.ist.pathwaymaps()
  • The group field for reference data is optional. If omitted, grouping uses the different y values.

IST 0.5.11

  • Essential tables are now ready in ist.results objects
  • Getter functions (e.g. getTabSignatures()) ease slot accession in ist.results objects
  • Added helpers to generate the tables

IST 0.5.10

  • Added first getters to retrieve results tables (TODO: unit testing)
  • Fixed minor bug in imports

IST 0.5.9

  • Added ist.results class for holding pathway results
  • Added fit() and show() methods

IST 0.5.8

  • Prepared parallel implementations of fitting and predicting ist.pathways
  • However, now the SerialParam backend is used due to MulticoreParam hanging for no apparent reason (probably missing exports)

IST 0.5.7

  • ist.pathways should accept a BiocParallel backend now for fit() and predict()
  • Added helper function with repeated logic for fitting ist.pathways

IST 0.5.6

  • Added a helper with the logic of applying fold changes to data matrices, as it is shared between some classes
  • Added predict() to ist.signatures

IST 0.5.5

  • Added fit() and show() method for ist.signatures
  • Now orthIDcon() is a unique interface for mapping within and between species
  • Added BiocParallel dependency

IST 0.5.4

  • Small change in sample.env.ist
  • Added new class ist.signatures to hold signatures from varios organisms

IST 0.5.3

  • Added new sample data sample.env.ist, more similar to what we are actually using IST on. Contains signatures from several organisms with metadata and pathways with metadata.

IST 0.5.2

  • Added defaults to OC models (as they were present for BIN)
  • Now OC should accept other kernels as well (untested)
  • Added a slot for models, storing the sample names used for training
  • Decisions have new columns: sample.intrain, sample.ref, sample.ist

IST 0.5.1

  • Fixed strange bug in NAMESPACE (watch out for this in the future), where do.isx would be exported as a S3 method called do. Now roxygen generates the correct file again
  • Minor changes

IST 0.5.0

  • Important API change: ref.y does not exist anymore. Now one can control the samples included in the models using id.oc, id.bin and those that are IST'd with id.ref and id.ist
  • TODO: make use of these in plot() and batch mode

IST 0.4.15

  • reduce.reg() can now wait for unfinished jobs and pass arguments to loadRegistry()

IST 0.4.14

  • The wrapper do.isx() does not return the models now, to save disk space and hopefully lower execution time in reduceResults()

IST 0.4.13

  • Updated the main README.md to give an overview of IST's purpose

IST 0.4.12

  • Fixed bug in get.de.genes() that would always restrict to 100 differential genes
  • Documented pathways.table.oc and pathways.table.bin in wrapper

IST 0.4.11

  • Seems like the 0.4.10 version batch jobs completed successfully (isd, isa, iss)
  • Fixed example for define()
  • Batch mode seems to work for pathway models

Comments:

  • If pathway models are going to be independent of the translator, they can be sped up by just fitting them once and then running all the translators on them. Might need another wrapper like do.isx().

IST 0.4.10

This version contains important changes on how the wrappers work. I am trying to have a common interface to avoid duplicated code. This is achieved by combining ellipsis and explicit arguments that are passed on, and leveraging the common define(), fit() and predict() API.

  • It is unclear whether batch model is working yet.
  • Removed duplicated entries in docs
  • Defined a way to create objects: define(). It is like new() but it can ignore mismatching arguments in ellipsis without throwing error.
  • Now do.isx() can run both ist.translator and ist.pathways.

IST 0.4.9

  • Fixed unit testing (change in behaviour of limma helper)
  • Fixed duplicated documented arguments
  • Fixed uses of 1:n
  • Fixed tabs (multiple of 4)
  • Removed lines of length >80
  • Updated documentation format
  • Added biocViews
  • Updated maintainer/author fields to be compliant
  • BiocCheck() gives 1W (set.seed) and 5N

IST 0.4.8

  • Batch jobs can now run isd, isa ans iss
  • Changed name of wrapper to run the three of them
  • Added imports from stats and utils
  • Helper to find DE genes will only return their ids by default, topTable can be obtained with a flag
  • Batch can run with and without list of de.genes
  • Jackknifing is not run by default on pls models

IST 0.4.7

  • Added statmod package for robust limma estimates

IST 0.4.6

  • Added limma for CI/CD
  • Now fit() triggers the DE genes analysis
  • Added unit testing in workflow
  • Fixed unit testing

IST 0.4.5

  • Added function to trigger limma analysis to find de.genes
  • Moved unit testing of defaults to their own file

IST 0.4.4

  • Fix bug where 0-confidence orthologs would make it through
  • Intra-species mapping now has same format as inter-species
  • Cleaned up log files

IST 0.4.3

  • Small fix to skip batch tests

IST 0.4.2

  • Added the required packages SummarizedExperiment, batchtools to CI/CD
  • Build ignores reg- and Meta directories

IST 0.4.1

This commit contains the very basics for batch analysis, focused on one flavour for now (ISD). This affects a good amount of files.

  • Main function: wrapper do.batch.isd()
  • Default SGE configuration files default.config.batch()
  • Helper for reducing: reduce.reg() (UNTESTED)
  • Added batch configuration files for regular job and e-mail notification (just works for my e-mail right now) in inst/templates
  • Basic examples and nit testing and basic submitter wrapping do.isd()
  • .gitignore will ignore directories starting by reg-

Other changes

  • Helpers now have a separate file from defaults

To do

  • Check if batch version is actually using predefined orthologs
  • Make sure no small files are left on the working directory (logs...)
  • Test the reduce function

IST 0.4.0

  • Added do.isd() wrapper, documented and with example

IST 0.3.14

  • fit.ist.translator() should re-use orthology mapping if provided
  • Added test case in workflow to cover this

IST 0.3.13

  • Removed mapOrthologs() function, was apparently a duplicate of orthIDcon() and was never called
  • Changed mistaken utils::new() to methods::new()

IST 0.3.12

  • Added the option to specify a proxy in the ortholog mapper orthIDcon(), checked the function arguments and added ellipsis

IST 0.3.11

  • Fixed .gitlab-ci.yml

IST 0.3.10

  • Still dealing with vignette prebuilt index
  • Info in github and in SO (link1 link2)
  • Now I think this warning is because of the --no-build-vignettes option
  • Modified the .gitlab-ci.yml file because the error said BiocStyle was not available
  • Importing utils because now new objects are created with utils::new()

IST 0.3.9

  • Trying to fix the following error in builder: Package has a VignetteBuilder field but no prebuilt vignette index.
  • Changed .Rbuildignore to not ignore ^doc$ and ^Meta$

IST 0.3.8

  • Added quickstart vignette by taking the example from data-raw/01_showcase.R

IST 0.3.7

  • Fixed small erorr in showcase
  • Small changes in .Rbuildignore, .gitignore
  • Now only 20 repeats in the binary model training (down from 100)

IST 0.3.6

  • Expanded example scripts to try batch jobs

IST 0.3.5

  • Expanded example data for testing purposes

IST 0.3.4

  • Fixed small bug for intra-species translators

IST 0.3.3

  • Added show method for ist.pathways

IST 0.3.2

  • Added predict method for ist.pathways

IST 0.3.1

  • Added fit for ist.pathways
  • Added pathways to the sample data

IST 0.3.0

  • Added ist.pathways class

IST 0.2.4

  • Small fix

IST 0.2.3

  • CI enabled

IST 0.2.2

  • The one-class model sets seeds as well
  • Seeds are optional now (can be useful for parallel jobs)

IST 0.2.1

  • Added helper functions to generate default parameters for binary classifiers, was particularly annoying to set up seeds in caret::train()
  • Removed internal data with defaults
  • Changed preProc to preProcess, it's unclear why this is referred to as both in the documentation (?train)
  • Seeds are controlled in the binary classifier, two approaches: with a seed argument, which calls to set.seed() before training, and using the seeds built-in argument in trainControl. Still have to check how this works in a parallel setup.

IST 0.2.0

  • Changed the validation scheme for the binary classifier
  • plsr - now uses caret and runs by default 100 rounds of repeated CV
  • Extra slot with the train object
  • Supress only the warning on regression using two values only
  • When fitting the final PLS, all the specified number of components will be fit (especially for scoreplot purposes); however, when predicting the decision, only the optimal Ncomp will be taken into account
  • By default, jackknifing is enabled on the final model

IST 0.1.23

  • Fixed bug in predict.ist.bin() that would not predict scores even if asked to do so
  • Added requirement on the checkmate package version

IST 0.1.22

  • Added plot method for scores and decision values
  • Doc and test updates

IST 0.1.21

  • Added the ref.y slot to iss to have traceability
  • Improved show

IST 0.1.20

  • Added true fold changes to sample data
  • Showcase is longer and has density plots
  • Improved documentation on fit and predict methods
  • Added show methods

IST 0.1.19

  • Now predict can give the scores of the pls models (isd/isa)
  • Defaults to 2 components
  • Added example (future vignette)

IST 0.1.18

  • Refactored type to flavour

IST 0.1.17

  • Small class refactoring
  • Fixed bug in predict

IST 0.1.16

  • Removed unnecessary file for predict method

IST 0.1.15

  • Added predict method for the discriminator

IST 0.1.14

  • Removed isc, now it is a particular case of isa
  • Changes to the class definitions (more checks, slot removal)
  • Primitive workflow already available
  • fit method for the discriminator that applies to all flavours

IST 0.1.13

  • Refactoring of class and methods names (were too long)

IST 0.1.12

  • Added a predict method for binary classifier

IST 0.1.11

  • Added class for the classifier model in ISS
  • Added a fit method for it

IST 0.1.10

  • Added a predict method for one-class

IST 0.1.9

  • Added class for the one-class model in ISS
  • Added a fit method for it

IST 0.1.8

  • Same as version 0.1.7 with the predict method

IST 0.1.7

  • Now the fit method is in its own file and better commented

IST 0.1.6

  • Added predict method for the translator
  • Modified the fit method, to join the mapping data.tables once only
  • Updated the format of the sample data
  • Updated unit testing

IST 0.1.5

  • Fixed fold change data frame (gene ids must be character)
  • Added fit method for the translator

IST 0.1.4

  • Added intra-organism mapper

IST 0.1.3

  • Added classes for translator and discriminator

IST 0.1.2

  • Added sample data
  • Fixed doc

IST 0.1.1

  • Modified DESCRIPTION
  • Added basic orthology mapper

IST 0.1.0

  • Initial addition of functions and tests