basejump 0.7.0 (2018-08-07)

In this release, we are migrating some of the S4 generics previously exported in the bcbioBase package. We are consolidating these functions here for simplicity and stability.

New functions

Major changes

  • Now using curl::has_internet() internally to check for Internet connection. This applies to the annotation functions that query web databases.
  • Added coercion method support for converting a SummarizedExperiment to an unstructured list. This is the method used internally for flatFiles().

basejump 0.6.4 (2018-08-03)

New functions

  • matchInterestingGroups(): New developer function to automatically handle interestingGroups argument used across various plotting functions and in the bcbio infrastructure packges.

basejump 0.6.3 (2018-08-01)

Minor changes

  • Migrated separatorBar and updateMessage global export from bcbioBase. Improved separatorBar appeareance to automatically scale to current session width, using getOption("width").

basejump 0.6.2 (2018-07-31)

New functions

  • convertSymbolsToGenes(): provides SummarizedExperiment method support for converting objects containing gene symbols (“geneName”) as rownames back to gene identifiers (“geneID”).
  • eggnog(): quickly download current annotations from EggNOG database. Useful for annotating gene-to-protein matches; currently in use with the brightworm RNAi screening package, which contains WormBase gene ID and EggNOG ID annotations.

Major changes

  • Now suggesting BiocManager instead of BiocInstaller for installation.
  • broadClass() now supports GRanges and SummarizedExperiment. Support for data.frame and/or DataFrame class objects has been removed.

Minor changes

basejump 0.6.1 (2018-07-21)

Minor changes

  • Bug fix for convertGenesToSymbols() method for SummarizedExperiment. Previously, if geneName column was a factor, this function would error. This issue has been fixed by ensuring that the symbols provided in geneName are coerced to a character vector.
  • Improved conda installation instructions.

basejump 0.6.0 (2018-07-17)

Major changes

Migrated functions

Previously, these functions were exported in the bcbioBase package, but they provide non-bcbio-specific functionality, and should be included here in the basejump package instead:

Providing basic SummarizedExperiment class method support for counts().

Minor changes

basejump 0.5.11 (2018-07-09)

Minor changes

  • Now requiring ggplot2 v3.0 internally.
  • theme_midnight() and theme_paperwhite() now extend ggplot2::theme_linedraw(), improving the consistency between these themes.
  • Example data is now consistenly formatted using snake case: rnaseq_counts and single_cell_counts, instead of the previous camel case conventions: rnaseqCounts, singleCellCounts.
  • Camel variants of the ggplot themes are now deprecated.
  • Updated internal gene synonyms data from NIH.

basejump 0.5.10 (2018-06-28)

Minor changes

  • Removed makeNames argument from readFileByExtension() function. Use the makeNames family of functions manually after data import instead. This helps avoid unwanted sanitization of data.
  • Simplified assert checks for internal load function.
  • Improved code coverage.
  • AppVeyor CI updates to work with Bioconductor 3.8 devel.

basejump 0.5.9 (2018-06-12)

Minor changes

  • Markdown function consistency improvements. Now all relevant Markdown functions use text as the primary argument, instead of object.

basejump 0.5.8 (2018-06-05)

Minor changes

Infrastructure changes

  • Reenable Travis CI blocklist, excluding develop branch from checks.
  • Reorganized documentation of deprecated and defunct functions.

basejump 0.5.7 (2018-05-24)

Minor changes

basejump 0.5.6 (2018-05-19)

Minor changes

basejump 0.5.5 (2018-05-15)

Major changes

Minor changes

basejump 0.5.4 (2018-05-08)

basejump 0.5.3 (2018-04-30)

Minor changes

basejump 0.5.2 (2018-04-26)

Minor changes

  • Improved documentation for assert check functions.
  • Deprecated geomean() in favor of geometricMean().
  • Simplified internal code for grepString().
  • Added message during hgnc2gene() call.
  • Miscellaneous documentation fixes.
  • Moved internal constructors into the S4 method definitions, where applicable.
  • Simplified default parameter definition for panther(organism = "XXX").
  • Improved code coverage, using nocov where appropriate.

basejump 0.5.1 (2018-04-16)

Minor changes

  • emptyRanges(): Now using match.arg() internally to capture seqname argument.
  • Removed legacy .assignCamelArgs() and .assignCamelFormals() internal functions.
  • Improved internal handling of XLSX files in localOrRemoteFile().

basejump 0.5.0 (2018-04-13)

New functions

  • emptyRanges() enables easy creation of placeholder ranges for GRanges objects, where transgene and FASTA spike-ins are needed.
  • hgnc2gene() enables easy mapping of HGNC to Ensembl gene identifiers.
  • mgi2gene() enables easy mapping of MGI to Ensembl gene identifiers.
  • panther() function enables easy querying of the PANTHER website. Human, mouse, nematode worm, and fruit fly are currently supported. The specific PANTHER release (e.g. 13) can be declared using the release argument. Otherwise, the function will return the most recent annotations from the PANTHER website.
  • Added isURL() check function.
  • readJSON() adds support for JSON files. Like the other read functions, it supports both local files and remote URLs.

ggplot2 themes

Major changes

  • loadData() now supports .rda, .rds, and .RData files. The function will error by design if multiple data extensions are detected inside the directory specified with the dir argument.

Minor changes

  • Consolidated assert check function code.
  • Moved assertive imports to basejump-package.R file.
  • Consolidated globals inside package to globals.R file.
  • Removed internal .biocLite() function. Now using requireNamespace() instead, without attempting to install automatically.
  • Added internal support for safe loading RDS files.
  • Switched back to using message(), warning(), and stop() instead of the rlang equivalents.
  • Improved internal method declaration using getMethod() where applicable.
  • multiassignAsEnvir() is now recommended in place of multiassignAsNewEnvir().
  • readFileByExtension() will now attempt to use the rio package for file extensions that are not natively supported.
  • writeCounts() now uses mapply() internally.
  • Migrated assertFormalAnnotationCol() to bcbioBase package.

basejump 0.4.0 (2018-03-22)

Major changes

  • Introducing new functions for the acquistion of gene and transcript annotations from Ensembl: ensembl(), genes(), and transcripts(). These functions allow the return of GRanges, DataFrame, and data.frame class objects from AnnotationHub using ensembldb.
  • Improved internal broadClass definition code to match against chromosome from Ensembl if available.
  • loadDataAsName() now works with unquoted names, improving consistency with loadData() (non-standard evaluation).

Minor changes

Deprecations

basejump 0.3.1 (2018-02-19)

  • Now exporting all assert checks in camel case instead of snake case, to match consistency in the rest of the package.
  • Added sanitizeColData() function.
  • Added assertAllAreNonExisting() function.
  • Now exporting midnightTheme() as a theme_midnight() alias to match the syntax in the ggplot2 package.
  • Added working examples and code coverage for all assert check functions.
  • Simplified the internal collapse code for annotable() to simply work on the Entrez identifier column (entrez). If a manually passed in data frame still has duplicates, the function will now abort instead of attempting to use collapseToString().
  • Added ggplot2 color palette assert checks: assertColorScaleContinuousOrNULL(), assertColorScaleDiscreteOrNULL(), assertFillScaleContinuousOrNULL(), assertFillScaleDiscreteOrNULL().

basejump 0.3.0 (2018-02-16)

  • Switch to using assertive internally for assert checks.
  • Now exporting these assert check functions: assert_formal_annotation_col(), assert_formal_color_function(), assert_formal_compress(), assert_formal_gene2symbol(), assert_formal_header_level(), assert_has_rownames(), assert_is_a_number_or_null(), assert_is_a_string_or_null(), assert_is_an_implicit_integer(), assert_is_an_implicit_integer_or_null() assert_is_an_integer_or_null(), assert_is_annotable(), assert_is_character_or_null(), assert_is_data.frame_or_null(), assert_is_gene2symbol(), assert_is_implicit_integer(), assert_is_implicit_integer_or_null(), assert_is_tx2gene(), has_rownames(), initializeDirectory(), is_implicit_integer().
  • Renamed md*() functions to markdown*().

basejump 0.2.1 (2018-02-07)

basejump 0.2.0 (2018-01-28)

  • Offloaded internal bcbio-specific code to new package named bcbioBase. Consequently, this makes the basejump package leaner, meaner, and easier to manage. The following functions are now exported in that package: bcbio(), checkInterestingGroups(), flatFiles(), interestingGroups(), metrics(), plotDot(), plotGene(), plotQC(), plotViolin(), prepareSummarizedExperiment(), prepareTemplate(), readDataVersions(), readLogFile(), readProgramVersions(), readSampleMetadataFile(), sampleMetadata(), sampleYAML(), sampleYAMLMetadata(), sampleYAMLMetrics(), and selectSamples(). These functions are now deprecated here in basejump (see deprecated.R file for more information).
  • comp() and revcomp() have been deprecated in favor of complement() and reverseComplement() from the Biostrings package.
  • Internally, errors, messages, and warnings now use methods from the rlang package: abort(), inform(), and warn(), in place of stop(), message(), and warning(), respectively.
  • Improved error handing for missing files in loadData(). Additionally, the file name must match the internal name in the RData file, otherwise loadData() will warn the user. This is more strict than the default behavior of base::load(), but helps prevent accidental overwrite in the current working environment.
  • localOrRemoteFile(), previously an internal function, is now exported.
  • annotable() now uses internal GRCh37 annotations from the annotables package, which is saved in the extdata/ directory internally. Previously, these genome annotations were accessed from lazy loaded data saved in the data/ directory of the package repository.
  • annotables() now checks for all packages attached by ensembldb and AnnotationHub and forces detachment at the end of the function call. Otherwise, this can result in the unwanted effect of ensembldb masking other user-loaded functions, such as the tidyverse suite (e.g. dplyr::select()).
  • Consistently reformatted code indents to be a multple of 4 spaces, as recommended by Bioconductor.
  • camel() now handles delimited numbers a little differently. Previously, delimiters in between numbers (e.g. the commas in “1,000,000”) were stripped. Sometimes this can result in confusing names. For example, if we have a column formatted in dotted case containing a decimal (e.g. “resolution.1.6”), the decimal would be stripped (e.g. “resolution16” in camel). Now, we sanitize a numeric delimiter as a lower case “x” character (e.g. “resolution1x6”). This ensures that numbers containing decimals remain semantically meaningful when sanitized with camel().
  • Internally, gsub() (and grepl()) calls have been simplified to use the default order of “pattern, replacement, x”.
  • Internally, all implicit integers have been converted to explicit integers, where applicable.

basejump 0.1.10 (2017-12-20)

  • Bug fix for multiplexed sample input into readSampleMetadataFile(). We were detecting the presence of index column but should instead check against sequence column.
  • Added dynamicPlotlist() and mdPlotlist() plotting utilities.
  • Added uniqueSymbols parameter to annotable() function.

basejump 0.1.9 (2017-12-18)

basejump 0.1.8 (2017-12-14)

basejump 0.1.7 (2017-12-11)

basejump 0.1.6 (2017-12-06)

basejump 0.1.5 (2017-12-05)

basejump 0.1.4 (2017-12-04)

basejump 0.1.3 (2017-12-01)

  • loadData() and loadDataAsName() now default to replace = TRUE. If an object with the same name exists in the destination environment, then a warning is generated.
  • collapseToString() only attempts to dynamically return the original object class on objects that aren’t class data.frame. I updated this code to behave more nicely with grouped tibbles (grouped_df), which are a virtual class of data.frame and therefore can’t be coerced using as(object, "grouped_df").
  • DNA sequence utility functions comp() and revcomp() now return NULL for integers and numerics.
  • For prepareSummarizedExperiment(), added support for dropping NULL objects in assays list. This is useful for handling output from bcbioRNASeq when transformLimit is reached. In this case, the rlog and vst matrices aren’t generated and set NULL in the assays list. Using Filter(Negate(is.null), assays) we can drop these NULL objects and prevent a downstream dimension mismatch in the SummarizedExperiment::SummarizedExperiment() call.
  • Improved support for multiplexed files in readSampleMetadataFile(). This now checks for a sequence column containing ACGT nucleotides. When those are detected, the revcomp column is generated. Otherwise this step is skipped. This is useful for handling multiplexed sample metadata from 10X Genomics Cell Ranger single-cell RNA-seq samples.
  • Updated annotable() function to include nested Entrez identifiers in the entrez column. This is useful for downstream functional analysis.

basejump 0.1.2 (2017-11-30)

basejump 0.1.1 (2017-11-11)

  • Added overwrite support for saveData(). Now will skip on existing files when overwrite = FALSE.
  • Bug fix for readDataVersions(), which shouldn’t have the column types defined, using col_types = "ccT".
  • Improved key value pair method for loadDataAsName(). Now rather than using a named character vector for the mappings argument, the user can simply pass the key value pairs in as dots. For example, newName1 = "oldName1", newName2 = "oldName2". The legacy mappings method will still work, as long as the dots argument is a length of 1.
  • Ensembl release version now defaults to NULL instead of current for annotable(), gene2symbol(), symbol2gene() and tx2gene() functions.
  • Allow rowData to be left unset in prepareSummarizedExperiment(). This is useful for setting up objects that don’t contain gene annotations.
  • Removed sample selection by pattern matching (pattern, patternCol arguments) in readSampleMetadata(). This feature wasn’t fully baked and doesn’t offer enough functionality to the user.

basejump 0.1.0 (2017-10-23)

  • Bump version to match bcbioRNASeq package.
  • Improved unit testing coverage of prepareSummarizedExperiment().
  • Added quiet mode support to functions that output messages, where applicable.
  • Consolidated roxygen2 function imports to basejump-package.R file.
  • Deprecated sampleDirs() generic.
  • Improved organism detection in detectOrganism() and added support for chicken genome.
  • Clarified warning messages in prepareSummarizedExperiment() to make sample loading with loadRNASeq() and loadSingleCell() in the bcbio packages less confusing.
  • Improved NULL returns in readDataVersions, readLogFile(), and readProgramVersions() utility functions.
  • Fixed export of *GTF() alias functions to simply wrap the *GFF() functions with S4 methods support.
  • Improved lane split technical replicate handling in readSampleMetadataFile().
  • Improved camel() syntax for both lax and strict modes. Added upperCamel() function.
  • Switched str_() to base grep() and gsub() in internal functions.

basejump 0.0.25 (2017-10-13)

  • Improved consistency of setMethod() calls using signature().
  • Converted loadRemoteData() to a standard function instead of using S4 dispatch, allowing the envir argument to be set properly.

basejump 0.0.24 (2017-10-10)

  • Added additional package version requirements in DESCRIPTION file.
  • Implicit integers are allowed.
  • Using GitHub version of covr package for unit tests.
  • Renamed multiassignAsNewEnv() to multiassignAsNewEnvir()
  • Added *GFF() function variants for gene2symbolFromGTF() and tx2geneFromGTF().
  • Added shared bcbio generic functions: aggregateReplicates(), bcbio(), bcbio<-(), interestingGroups(), metrics(), plotGene(), sampleDirs(), sampleMetadata(), selectSamples(). These functions are saved in bcbioGenerics.R file.
  • Incorporated bcbio utility functions shared across bcbioRNASeq and bcbioSingleCell: readDataVersions() (deprecated .dataVersions()), readLogFile() (deprecated .logFile()), readProgramVersions() (deprecated .programs()), sampleYAML() (deprecated .sampleYAML()), sampleYAMLMetadata() (deprecated sampleYAMLMetadata()), sampleYAMLMetrics() (deprecated .sampleYAMLMetrics()`).
  • Deprecated metadataTable() function.
  • Moved all roxygen2 documentation to methods-*.R files where applicable.
  • Now using assays in prepareSummarizedExperiment() generic definition as primary object.
  • Improved assignAndSaveData() to add silent return of file path.
  • Now consistently using clear function definitions (()) in chain operations with magrittr pipe (%>%).
  • Added .prepareSampleMetadata() utility function, for use with loading sample metadata from an external CSV, Excel, or YAML file.
  • Added loadData() functionality back to the package.
  • Initial commit of loadDataAsName() function.
  • Improved annotable() function documentation and support for Ensembl release versions.
  • Improved sanitization rules for camel(), dotted(), and snake() name functions. Added the strict argument to camel() and dotted().
  • Improved the documentation for the makeNames functions, by splitting each into their own separate methods file.
  • Improved S4 method support for the logRatio functions.
  • Added integer support for geomean() function. Also improved internal code of geomean() based on Paul McMurdie’s Stack Overflow post. See function documentation for more information.
  • Added release support for tx2gene functions.
  • Reduced the number of reexported functions (for documentation) down to the magrittr pipe (%>%), Matrix(), DataFrame(), and tibble().
  • Added silent return of file path to saveData() function.
  • Improved documentation for tibble coercion using as(object, "tibble")
  • Renamed collapse() function to collapseToString(), to avoid NAMESPACE collisions with tidyverse packages (dplyr, glue).

basejump 0.0.23 (2017-09-14)

basejump 0.0.22 (2017-09-08)

  • Improved unit testing coverage.
  • Renamed prepareSE() to prepareSummarizedExperiment(). Improved row and column name handling in the function. It now outputs more helpful diagnostic messages on error.
  • Reworked and simplified detectHPC() function to allow for unit testing.

basejump 0.0.21 (2017-09-01)

  • NAMESPACE improvements. Reduced the number of re-exported functions to simplify the package.
  • Improved code coverage and unit testing with additional testthat checks. Specifically, added unit testing for remote download functions and improved testing for GTF file utilities.
  • Code coverage now above 90%!
  • Renamed packageSE() to prepareSE() for better semantic meaning.
  • Made multiple generics more flexible by inclusion of passthrough ().
  • Reduced the number of deprecated functions.
  • Initial commit of internal localOrRemote() utility function.
  • Initial commit of prepareTemplate() function.
  • Added additional data-raw/ scripts.
  • Added onLoad.R script back to ensure proper attachment of annotables data package.
  • Removed tidyverse S4 method support.
  • Improved remote file handling for readFileByExtension(), readGTF(), and readYAML() functions.

basejump 0.0.20 (2017-08-16)

  • Offloaded devtools functions to personal package.
  • Upgraded all functions to S4 functions where possible.
  • Assign utilities were kept as S3 functions since S4 dispatch makes parent.frame() assignment not work correctly.
  • Deprecated snake case and British spelling variants to reduce the number of exported functions.
  • Added more working examples.
  • Added unit testing for annotables functions.

basejump 0.0.19 (2017-07-24)

  • Improved documentation and consistency with bcbio packages.
  • Improved integration of gene annotation calls using annotables package.

basejump 0.0.18 (2017-07-24)

basejump 0.0.17 (2017-07-11)

basejump 0.0.16 (2017-06-28)

  • Minor NAMESPACE updates while working on bcbio packages.
  • Tweaks for tidyverse S4 generic verbs. In particular, as_tibble() now provides better consistency for rowname conversion.

basejump 0.0.15 (2017-06-18)

  • Added testthat support for lintr checks.
  • Added S4 generic for as_tibble().

basejump 0.0.14 (2017-06-13)

  • dplyr 0.7 NAMESPACE fixes and function tweaks.

basejump 0.0.13 (2017-06-12)

  • setMethod() for tidyverse NAMESPACE collisons (dplyr, tidyr) using `signature(“data.frame”).

basejump 0.0.12 (2017-05-25)

  • Updated exports based on wormbase package.

basejump 0.0.11 (2017-05-18)

  • Improved naming functions to dynamically handle character vectors and objects that support naming assignments.
  • Added removeNA() utility function.

basejump 0.0.10 (2017-05-14)

  • Added NAMESPACE utilities to deal with tidyverse generic verbs.
  • Switched package documentation method to use roxygen2 with pkgapi.

basejump 0.0.9 (2017-05-13)

  • Added snake case function variants.

basejump 0.0.8 (2017-05-13)

basejump 0.0.7 (2017-0422)

  • Bug fixes for dplyr 0.6.0 update and improved kable handling.

basejump 0.0.6 (2017-04-14)

  • Dependency fix for successful compilation on the HMS RC Orchestra cluster.

basejump 0.0.5 (2017-04-12)

  • Consolidated functions in the documentation.

basejump 0.0.4 (2017-04-07)

  • Improved documentation.

basejump 0.0.3 (2017-03-22)

  • Removed dependencies and transfer functions to bcbioRNASeq.

basejump 0.0.2 (2017-03-22)

  • Added bcbio data import functions.
  • Added ggplot2 wrapper functions for quality control.

basejump 0.0.1 (2017-03-17)

  • Initial draft release.