Changelog

Source: NEWS.md

snpEnrichment 1.8.0 Unreleased

Minor improvements and fixes

  • In R/*estimate_ethnicity*.R,
    • use tidy style.
  • In DESCRIPTION,
    • a little change in Title and Description to clearly state the package uses a sampling approach.
    • setup package to use roxygen2.

snpEnrichment 1.7.0 2015-10-01

  • NAMESPACE: Update to fix warnings from R CMD check using R version 3.2.2.
  • DESCRIPTION: Update according to new imports in NAMESPACE.

snpEnrichment 1.6.6 Unreleased

  • NAMESPACE: Update to fix warnings from R CMD check using R version 3.2.2.
  • R/enrichment.R: Update ‘plot’ method to fix global definition warnings.

snpEnrichment 1.6.5 Unreleased

  • tests/RUN-TEST_snpEnrichment.R: Add a test script.

snpEnrichment 1.6.4 Unreleased

  • R/enrichment.R: Update ‘getEnrichSNP’ to add information about related eSNP for xSNP.

snpEnrichment 1.6.3 2015-02-09

  • DESCRIPTION: Change maintainer email.
  • R/enrichment.R: Minor changes.

snpEnrichment 1.6.2 Unreleased

  • R/enrichment.R: Minor changes.
  • R/chromosome.R: Minor changes.
  • R/Global.R: Minor changes.

snpEnrichment 1.6.1 Unreleased

  • R/enrichment.R: Minor changes.

snpEnrichment 1.6.0 2014-11-04

  • R/Global.R: Fix a bug in ‘compareEnrichment’ method with parameter ‘empiricPvalue=TRUE’.

snpEnrichment 1.5.10 Unreleased

  • R/Global.R: Fix a glitch in ‘readEnrichment’. Sometimes chromosomes 10 and 20 are read respectively instead of 1 and 2.
  • R/Global.R: Some minor changes.

snpEnrichment 1.5.9 Unreleased

  • data/toyEnrichment.RData: Minor changes.
  • R/Global.R: Add internal function ‘.splitByChrom’. User is now allowed to use a single file in ‘snpListDir’ for ‘readEnrichment’ function.
  • man/snpEnrichment-internal.Rd: Update according to R code changes.
  • man/readEnrichment.Rd: Update according to R code changes.

snpEnrichment 1.5.8 Unreleased

  • R/enrichment.R: Update ‘print’ method to print results according to the parameter ‘empiricPvalue’ in ‘reSample’ function.
  • R/enrichment.R: Update ‘compareEnrichment’ according to changes in ‘print’ method.
  • R/chromosome.R: Some minor changes.
  • man/compareEnrichment.Rd: Update according to R code changes.
  • man/print-methods.Rd: Update according to R code changes.

snpEnrichment 1.5.7 Unreleased

  • R/*.R: Add function ‘getEnrichSNP’ and some minor corrections.
  • man/*.Rd: Update according to R code changes and some corrections.
  • NAMESPACE: Updata according to R code changes.
  • inst/example.R: Update ‘excludeFile’ list according to changes in ‘toyEnrichment’ and ‘extdata’.
  • man/snpEnrichment-package.Rd: Update ‘excludeFile’ list according to changes in ‘toyEnrichment’ and ‘extdata’.
  • man/excludeSNP-methods.Rd: Update ‘excludeFile’ list according to changes in ‘toyEnrichment’ and ‘extdata’.
  • README.md: Update ‘excludeFile’ list according to changes in ‘toyEnrichment’ and ‘extdata’.

snpEnrichment 1.5.6 Unreleased

  • R/Global.R: ‘readEnrichment’ works with at least one snp list in ‘snpListDir’.
  • R/Global.R: Fix ‘mclapply2’ under operating systems which are not Linux.
  • R/Global.R: Fix ‘maxCores’ under operating systems which are not Linux.
  • man/snpEnrichment-package.Rd: Update example.
  • inst/example.R: Update according to changes in ‘snpEnrichment-package.Rd’.
  • README.md: Update according to changes in ‘snpEnrichment-package.Rd’.
  • R/*.R: the “types” parameter is renamed “type”.
  • man/*.Rd: Update according to R code changes.

snpEnrichment 1.5.5 Unreleased

  • man/*.Rd: Replace ‘summary’ by ‘print’.
  • inst/example.R: Replace ‘summary’ by ‘print’ according to changes in ’*.Rd’ files.
  • README.md: Replace ‘summary’ by ‘print’ according to changes in ’*.Rd’ files.

snpEnrichment 1.5.4 Unreleased

  • R/*.R: Change default value for ‘empiricPvalue’ parameter to ‘TRUE’.
  • man/*.Rd: Update according to R code changes.
  • inst/example.R: Update according to R code changes.
  • README.md: Update according to R code changes.
  • R/enrichment.R: Change warning messages in ‘compareEnrichment’.

snpEnrichment 1.5.2 Unreleased

  • R/Global.R: Add some internal functions to check files needed by ‘initFiles’, ‘writeLD’ and ‘readEnrichment’ functions.
  • man/snpEnrichment-internal.Rd: Update according to R code changes.
  • inst/example.R: Update according to R code changes.

snpEnrichment 1.5.1 Unreleased

  • R/Global.R: Internal function ‘maxCores’ handle warnings on macintosh system.
  • R/Global.R: Handle warning / error in ‘initFiles’ when ‘snpInfoDir’ or ‘signalFile’ are missing or invalid.

snpEnrichment 1.5.0 Unreleased

  • R/Global.R: Fix a bug in ‘compareEnich’ when ‘xSNP’ was missing in "object.*".
  • man/*.Rd: Some corrections in example.

snpEnrichment 1.4.3 Unreleased

  • man/*.Rd: Update according to R code changes.

snpEnrichment 1.4.2 Unreleased

  • R/enrichment.R: Fix a bug when ‘xSNP’ field is empty in ‘plot’ method.
  • R/Global.R: Fix ‘options(stringsAsFactors=FALSE)’ in ‘writeLD’.
  • man/snpEnrichment-package.Rd: Update according to DESCRIPTION file.

snpEnrichment 1.4.1 Unreleased

  • R/*.R: Minor optimizations.
  • R/enrichment.R: Fix a bug in ‘plot’ method with ‘ggplot=TRUE’.

snpEnrichment 1.4.0 Unreleased

  • R/Global.R: Change internal functions used by ‘readEnrichment’ and ‘writeLD’.
  • R/Global.R: Improvment in ‘writeLD’ function.
  • R/Global.R: Add ‘depth’ parameter in ‘writeLD’ function.
  • R/Global.R: Minor optimizations.
  • R/enrichment.R: Fix a bug when ‘object’ was not updated properly, with ‘reSample’ function and all defaults parameters.
  • R/*.R: Remove ‘extendMethod’ parameters from all functions.
  • data/: Remove ‘toyEnrichmentM2.RData’.
  • data/: Rename ‘toyEnrichmentM1.RData’ to ‘toyEnrichment.RData’
  • man/*.Rd: Update according to R code changes.

snpEnrichment 1.3.12 Unreleased

  • R/*.R: Minor changes in R code.
  • R/Global.R: Remove parameter ‘snpListDir’ in ‘initFiles’ function.
  • R/Global.R: Fix ‘ldThresh’ parameter in ‘initFiles’ function.
  • man/*.Rd: Update according to R code changes.

snpEnrichment 1.3.11 Unreleased

  • R/enrichment.R: Add ‘pvalue’ parameters in ‘plot’ method.
  • R/plot-methods.Rd: Update according to R code changes.

snpEnrichment 1.3.10 Unreleased

  • R/*.R: Add ‘empiricPvalue’ arguments in order to choose if p-values should be empirical or based on null distribution (resampling).

snpEnrichment 1.3.9 Unreleased

  • R/Enrichment.R: Prevent a bug in ‘plot’ method with ‘ggplot=TRUE’.

snpEnrichment 1.3.8 Unreleased

  • R/*.R: Minor changes in R code.
  • R/Global.R: Fix a missing square root in Z statistics computation.
  • R/enrichment.R: Fix legend position in ‘plot’ for ‘ggplot=TRUE’.

snpEnrichment 1.3.7 Unreleased

  • R/*.R: Minor changes in R code.
  • R/Global.R: Change p-value computation in ‘.reSample’ and ‘compareEnrich’ functions.
  • R/Global.R: Convergence control on Z statistic is removed in ‘.reSample’ and ‘compareEnrich’ functions.

snpEnrichment 1.3.6 Unreleased

  • R/*.R: Minor changes in R code.
  • R/enrichment.R: ‘compareEnrichment’ now returns ‘object.x’, ‘object.y’ and object from comparison.
  • R/compareEnrichment.Rd: Update according to R code changes.

snpEnrichment 1.3.5 Unreleased

  • R/*.R: Minor changes in R code.
  • R/enrichment.R: Fix an error in ‘reSample’ method that occurs in ‘compareEnrichment’ method.
  • R/enrichment.R: Add controls on installed packages for ‘ggplot=TRUE’ in plot method.
  • R/enrichment.R: Remove convergence control in ‘reSample’ when ‘Resampling’ slot are empty in ‘compareEnrichment’. ‘compareEnrichment’ now performs ‘nSample’ resampling for ‘object.x’, ‘object.y’ and for comparison.
  • R/global.R: Remove ‘while’ loop in ‘.compareEnrich’ (not used yet).

snpEnrichment 1.3.4 Unreleased

  • R/*.R: Minor changes in R code.
  • man/compareEnrichment.Rd: Add alias for signature “Enrichment”.

snpEnrichment 1.3.3 Unreleased

  • R/enrichment.R: Fix a bug in ‘excludeSNP’ when ‘LD’ is set to ‘FALSE’.

snpEnrichment 1.3.2 Unreleased

  • R/enrichment.R: Redefine ‘print’ method for ‘Enrichment’ object.
  • R/chromosome.R: Redefine ‘print’ method for ‘Chromosome’ object.

snpEnrichment 1.3.1 Unreleased

  • R/Global.R: ‘readEnrichment’ returns an error when ‘initFiles’ was not run before.
  • R/enrichment.R: ‘reSample’ method for ‘Enrichment’ object now reruns one warning when ‘mc.cores’ is decreased.
  • R/enrichment.R: call for ‘reSample’ method is saved properly in ‘Enrichment’ object.
  • R/enrichment.R: Redefine ‘plot’ method for ‘Enrichment’ object. ‘plot’ method can use ggplot2, if ‘ggplot’ is set to ‘TRUE’.
  • man/*.Rd: Update documentations files according to R code modification.

snpEnrichment 1.3.0 Unreleased

  • R/Global.R: ‘readEnrichment’ can deal with ld files computed with plink directly.

snpEnrichment 1.2.3 Unreleased

  • man/EnrichSNP-class.Rd: Add alias for method ‘[’ and ‘[’ with signature = ‘EnrichSNP,ANY,ANY,ANY’.
  • man/Chromosome-class.Rd: Add alias for method ‘[’ and ‘[’ with signature = ‘Chromosome,ANY,ANY,ANY’.
  • man/Enrichment-class.Rd: Add alias for method ‘[’ and ‘[’ with signature = ‘Enrichment,ANY,ANY,ANY’.
  • R/Global.R: Now use ‘read.plink’, ‘col.summary’, ‘ld’ from ‘snpStats’ package for read plink files and compute MAF and LD.
  • R/Enrichment.R: Fix ‘show’ method in order to deal with new parameters in ‘readEnrichment’ and ‘reSample’ functions.
  • R/*.R: Change default setting for ‘mc.cores’ to 1.
  • man/*.Rd: Update documentations files according to R code modification.

snpEnrichment 1.2.2 Unreleased

  • R/*.R: Change name of ‘SNP’ class to ‘EnrichSNP’.
  • R/*.R: Some improvements and computation time optimisations.
  • R/Global.R: Add ‘ldDir’ parameter in ‘writeLD’ which allow to choose the directory where LD files should be written.
  • R/Global.R: Add ‘ldDir’ parameter in ‘readEnrichment’.
  • R/Global.R: ‘initFiles’ now write and clean tempory files used by ‘readEnrichment’.
  • R/Global.R: Now LD is only computed by ‘writeLD’. Not anymore by ‘initFiles’.
  • R/Global.R: Remove ‘ldThresh’ and ‘LD’ parameters from ‘initFiles’.
  • R/Global.R: Remove ‘signalFile’, ‘transcriptFile’, ‘snpInfoDir’, ‘distThresh’, ‘LD’, ‘ldThresh’, ‘sigThresh’, ‘MAFpool’ and ‘extendMethod’ parameters from ‘compareEnrichment’.
  • R/enrichment.R: Remove ‘signalFile’, ‘transcriptFile’, ‘snpInfoDir’, ‘distThresh’, ‘LD’, ‘ldThresh’, ‘sigThresh’, ‘MAFpool’ and ‘extendMethod’ parameters from ‘compareEnrichment’.
  • R/enrichment.R: Fix issue for the whole genome convergence plot in ‘plot’ methods. Add parameter ‘onlyGenome’.
  • man/*.Rd: Update documentations files according to R code modification.

snpEnrichment 1.2.1 Unreleased

  • R/*-class.R: Add ‘print’ methods (same as ‘show’).
  • R/Global.R: Add error messages when files can not be created by ‘initFiles’.
  • R/Global.R: Remove ‘require(parallel)’ from ‘mclapply2’ function.
  • exdata/*: Move all external data to ‘inst’ directory in order to be used in examples.
  • man/*.Rd: Update documentations files according to R code modification.

snpEnrichment 1.2.0 Unreleased

  • R/enrichment.R: Add ‘onlyGenome’ parameter, which allow to compute the resampling step at chromosome level and genome or only at genome level.
  • R/enrichment.R: Fix ‘plot’ methods for low number of resampling.
  • R/enrichment.R: Change ‘Parameters’ to “Call”.
  • R/enrichment.R: ‘show’ is available for ‘Call’ slot.
  • R/enrichment.R: Remove ‘sigThresh’ and ‘extendMethod’ parameters from “reSample” method with ‘signature=“Enrichment”’.
  • R/enrichment.R: Remove ‘sigThresh’ and ‘extendMethod’ parameters from “excludeSNP” methods.
  • R/enrichment.R: Fix abscisse according to ‘nSample’. Abscisse origin is now equal to three.
  • R/enrichment.R: ‘chrNumber’ is replaced by ‘chr’, in ‘plot’ method for ‘Enrichment’ object.
  • R/Global.R: Fix bug in ‘compareEnrichment’ when some fields were not reseted with the option ‘onlyGenome=TRUE’.
  • R/Global.R: Remove ‘onlySignal’ parameter from ‘writeLD’ function.
  • R/Global.R: Change ‘Parameters’ to “Call”.
  • R/Global.R: Remove ‘sigThresh’ and ‘extendMethod’ parameters from “excludeSNP” methods.
  • NAMESPACE: Fix ‘NAMESPACE’ with missing ‘SNP’ class and methods.
  • data/*: Generate new toy datasets.
  • extdata/*: Generate new external datasets (iles needed to run the examples for the packages functions).
  • man/*.Rd: Update documentations files according to R code modification.

snpEnrichment 1.1.4 Unreleased

  • R/enrichment.R: Now results from method ‘compareEnrichment’ are the enrichment object and the summary table.
  • R/enrichment.R: ‘nSample’ in ‘excludeSNP’ can be equal to 0.
  • R/Global.R: ‘maxCores’ return at least 1.
  • R/mclapply2.R: run in parallel mode with at least 1 core.

snpEnrichment 1.1.3 Unreleased

  • R/Global.R: Some improvements and changes of functions: ‘initFiles’, ‘.writeSignal’, ‘writeLD’.

snpEnrichment 1.1.2 Unreleased

  • R/Global.R: Add informations about snp losses on each step of the algorithm.
  • R/Global.R: Fix minor bugs in read functions.

snpEnrichment 1.1.1 Unreleased

  • man/plot-methods.Rd: Corrects the description of method plot.

snpEnrichment 1.1.0 Unreleased

  • R/Global.R: Some minor code optimization and simplification.
  • R/Global.R: The method ‘excludeSNP’ now exclude the extended list of SNP provided in ‘excludeFile’. Note: ‘excludeFile’ can be a character vector with SNPs or a file path which contains a SNPs list.
  • R/Global.R: The function ‘writeLD’ now compute Linkage Disequilibrium for all SNPs in reference data or only for SNPs in signal.
  • R/enrichment.R: The slot ‘Signal’ of Enrichment object is replaced by slot ‘Loss’. This slot gives information about data losses (e.g. SNPs removed).
  • R/Global.R: Add ‘plot’ method for Enrichment object. This method show the convergence of Z statistics. Z statistic is scaled and centered in order to compare the convergence in chromosomes/genome.
  • R/Global.R: Fix a bug where some SNP which are not in reference data (‘snpInfoDir’) were not extended with SNP in LD.
  • R/Global.R: Fix bug for the extend method ‘LD block’ where SNPs which are not in linkage with another SNP, are removed.
  • man/*.Rd: Update Rd files with the R code correction.

snpEnrichment 1.0.2 Unreleased

  • R/Global.R: Matrix or data.frame are not anymore evaluated in the slot ‘Parameters’ of Enrichment object.
  • R/enrichment.R: Fix errors that occurred when the SNP list is too low in ‘reSample’ function.
  • R/enrichment.R: Fix an error that occured in ‘compareEnrichment’, when non-resampled Enrichment objects are given in the list fields.

snpEnrichment 1.0.1 Unreleased

  • R/Global.R: Some minor code optimization and simplification.
  • R/enrichment.R: The method ‘summary’ is not anymore masked by loading ‘snpEnrichment’ package.