Changes in version 1.23.2: o Add a function to coerce a GenotypeData object to a VCF object for use with VariantAnnotation. Changes in version 1.23.1: o Move ncdf4 from Imports to Suggests. Users who wish to use NetCDF files instead of GDS will have to install the ncdf4 package separately. This change eliminates the requirement to install the NetCDF library on Linux machines for users who plan to use GDS only. Changes in version 1.21.1: o Replace ZIP_RA with LZMA_RA for GDS compression. o Default is no compression for genotypes. Changes in version 1.19.1: o Speed up corr.by.snp in duplicateDiscordance. Changes in version 1.17.9: o Replace ncdf with ncdf4 o Deprecate plinkToNcdf and convertVcfGds (use SNPRelate functions instead) o Add function kingIBS0FSCI to define expected IBS0 spread of full siblings based on allele frequency. Changes in version 1.17.8: o do not compute qbeta for all points in qqPlot if thinning Changes in version 1.17.7: o add error handling to close GdsGenotypeReader and GdsIntensityReader gds files if they fail the validity method check Changes in version 1.17.6: o Use ZIP_RA as default compression in GDS files for faster access to compressed data Changes in version 1.17.5: o bug fix in checkImputedDosageFile if not writing a log file of missing values and an entire sample is missing from the file Changes in version 1.17.4: o bug fix for coloring truncated points in manhattanPlot Changes in version 1.17.3: o added support for hard-calling genotypes from imputed genotype probabilities in imputedDosageFile Changes in version 1.17.1: o changed colors for ibdPlot Changes in version 1.15.16: o added permute argument to exactHWE Changes in version 1.15.15: o allow multiple color schemes for plots color-coded by genotype Changes in version 1.15.13: o pedigreePairwiseRelatedness identifies great grandparent/great grandchild (GGp) and grand avuncular (GAv) Changes in version 1.15.12: o allow character scanID in createDataFile Changes in version 1.15.11: o added col argument to manhattanPlot Changes in version 1.15.10: o createDataFile converts non-finite values to NA. Changes in version 1.15.8: o alleleFrequency includes scans with missing sex. Changes in version 1.15.7: o Added option to reorder samples in vcfWrite. Changes in version 1.15.5: o Added option to read genotypes coded with nucleotides in createDataFile. Changes in version 1.15.3: o Added beta and standard error for GxE term to assocRegression output. Changes in version 1.15.2: o Added number of cases and controls to assocRegression output. Changes in version 1.15.1: o Added "ci" argument to qqPlot function. Changes in version 1.13.27: o Added "snpID" and "scanID" arguments to getGenotypeSelection. Changes in version 1.13.26: o Added getScanAnnotation, getSnpAnnotation accessors for GenotypeData objects. Changes in version 1.13.24: o Added data tables for genome build 38: centromeres.hg38.RData, pseudoautosomal.hg38.RData, HLA.hg38.RData, pcaSnpFilters.hg38.RData. Changes in version 1.13.23: o convertGdsNcdf works for transposed (sample x snp) genotype files. Changes in version 1.13.22: o Removed "outfile" arguments from batchChisqTest, batchFisherTest, and mendelErr. Saving output to a file should happen outside the function calls. o batchChisqTest and batchFisherTest have snp.include arguments to run on individual SNPs. Using batchFisherTest with this argument is recommended to replace the deprecated assocTestFisherExact. Changes in version 1.13.21: o assocRegression replaces assocTestRegression. Only one model is allowed per function call. o assocCoxPH replaces assocTestCPH. Output format is now similar to assocRegression. o exactHWE replaces gwasExactHWE. o assocRegression, assocCoxPH, and exactHWE include the option to select blocks of SNPs by index for easier parallelization. o scan.chromosome.filter is no longer an option; use setMissingGenotypes to filter data prior to running other functions. Changes in version 1.13.9: o Add use.names argument to getGenotype and getGenotype selection o Add order=c("file", "selection") argument to getGenotypeSelection o duplicateDiscordanceAcrossDatasets and dupDosageCorAcrossDatasets will not match on unmapped SNPs Changes in version 1.13.8: o Add drop=TRUE argument to getVariable, etc. Changes in version 1.13.7: o Add dupDosageCorAcrossDatasets. o Add getGenotypeSelection method to MatrixGenotypeReader. Changes in version 1.13.6: o Add getGenotypeSelection to select non-continguous SNPs and scans from GDS files. Changes in version 1.13.3: o Bug fix in imputedDosageFile - for IMPUTE2, include columns from .samples file in output scan annotation. Changes in version 1.11.33: o Allow getting variables from sub-nodes in a GDS file (e.g., getVariable(GdsReader, "snp.annot/qual")). o Add getNodeDescription method to GdsReader. o Added examples of converting from PLINK and VCF in Formats vignette. Changes in version 1.11.32: o imputedDosageFile replaces ncdfImputedDosage and gdsImputedDosage Changes in version 1.11.31: o setMissingGenotypes replaces ncdfSetMissingGenotypes and gdsSetMissingGenotypes Changes in version 1.11.22: o convertNcdfGds and convertGdsNcdf will convert files with any variable names (not just genotype) Changes in version 1.11.21: o Fixed bug in vcfWrite to output missing data code for ID column o Data cleaning vignette uses createDataFile instead of ncdfCreate and ncdfAddData o Data cleaning vignette uses snpgdsOpen and snpgdsClose Changes in version 1.11.20: o Fixed bug in assocTestCPH when there is no Y chromosome in the data Changes in version 1.11.19: o convertNcdfGds will not write entire snp and sample annotations to file o createDataFile replaces ncdfCreate and ncdfAddData Changes in version 1.11.18: o patch from Karl Forner to allow use of open gds objects in constructors for GdsReader and GdsGenotypeReader Changes in version 1.11.17: o removed duplicated .probToDosage function from ncdfImputedDosage.R source file Changes in version 1.11.16: o expanded matching options in duplicateDiscordanceAcrossDatasets Changes in version 1.11.15: o allowed truncate to be a numeric value or TRUE in qqPlot Changes in version 1.11.14: o added pasteSorted function Changes in version 1.11.13: o in case of missing allele code, return character genotype as NA Changes in version 1.11.12: o bug fix in assocTestRegression when a block contains only 1 SNP Changes in version 1.11.11: o added vcfCheck function to compare VCF file to GenotypeData object Changes in version 1.11.10: o bug fix in gwasExactHW when a block contains only 1 genotype Changes in version 1.11.9: o changed colors of BAF plots so points can be more easily distinguished Changes in version 1.11.8: o added ref.allele option to vcfWrite to select either A or B as the reference allele for each SNP Changes in version 1.11.7: o added vcfWrite function to write VCF file from GenotypeData object Changes in version 1.11.6: o bug fix in qqPlot, manhattanPlot when requesting thinning when bins only have 1 point Changes in version 1.11.5: o added pointsPerBin argument to manhattanPlot Changes in version 1.11.4: o added optional thinThreshold argument to manhattanPlot and qqPlot functions Changes in version 1.11.3: o updated gdsSubset for new gdsfmt read.gdsn syntax (also changed in release version) Changes in version 1.11.1: o Added ylim argument to qqPlot. Changes in version 1.9.9: o added block size support for GDS files stored with scan,snp dimensions o gdsSubset and gdsSubsetCheck now operate on the fastest dimension of the GDS file Changes in version 1.9.8: o updates/bug fixes to gdsSubset/gdsSubsetCheck - different missing value attributes may be set if sub.storage type is different. Changes in version 1.9.7: o Added gdsSubset and gdsSubsetCheck functions to make a subset GDS file that includes only specified SNPs and scans from an existing GDS file o Updated gdsImputedDosage and gdsCheckImputedDosage to account for IMPUTE2 gprobs files that have missing values (specified by three equal probability strings) o Updated gdsCheckImputedDosage to produce optional logfile reporting any missing genotypes Changes in version 1.9.6: o Revised anomFilterBAF - fewer centromere spanning anomalies that aren't real, corrects some merging issues (previously it would merge sections that really were different split widths). Users should be aware that this will increase running time. Changes in version 1.9.5: o Remove defunct functions. o Improve efficiency of gwasExactHW, mendelErr, assocTestRegression (reduce number of calls to rbind). Changes in version 1.9.4: o Bug fix in getChromosome method for SnpAnnotationDataFrame (proper behavior of unnamed "index" argument). Changes in version 1.9.3: o Added gdsImputedDosage function. o GdsGenotypeReader can return transposed genotypes. Changes in version 1.9.2: o ScanAnnotationDataFrame and ScanAnnotationSQLite allow non-integer scanID. o Fix getAlleleA and getAlleleB in GdsGenotypeReader to work with indels. Changes in version 1.9.1: o Documentation now located in vignettes/ folder. o Added ibdAssignRelationshipsKing. o Added support for genotype GDS files with scan x snp dimensions in GdsGenotypeReader. Changes in version 1.7.8: o Added gdsSetMissingGenotypes, updated argument names in ncdfSetMissingGenotypes. o Changed colorscheme in manhattanPlot.R. o Bug fix in ibdPlot - diagonal orange bars are back. o Bug fix in plinkWrite for writing just one sample. o Bug fix in printing pedigreeCheck error message. Changes in version 1.7.7: o Changed handling of GxE interaction variables in assocTestRegression. Changes in version 1.7.6: o Updated vignette for SNPRelate 0.9.16. Changes in version 1.7.5: o gwasExactHW will run on all chromosomes except (Y,M), rather than (autosome,X,XY) only. Changes in version 1.7.4: o More informative error messages in anomDetectBAF and anomDetectLOH. Changes in version 1.7.3: o Changed labeling of IBD plots from "HS" to "Deg2" and "FC" to "Deg3." o Bug fix in pedigreePairwiseRelatedness - no more warning about multiple values passed to stringsAsFactor. o pedigreeClean and pedigreeFindDuplicates are now defunct. Use pedigreeCheck instead. Changes in version 1.5.9: o assocTestRegression computes allele counts separately for each model. o convertNcdfGds uses information from a SnpAnnotationDataFrame to store allele and chromosome codes in the GDS file. Changes in version 1.5.8: o Adding missing value support to GdsReader. o Fixed bug in getAttribute method for GdsReader. o Updated GdsReader for compatibility with gdsfmt 0.9.11 (no longer compatible with older versions). Changes in version 1.5.7: o Fixed bug in genotypeToCharacter that resulted in calls to getGenotype(char=TRUE) for a single SNP to return NA. o Renamed minorAlleleSensitivitySpecificity to minorAlleleDetectionAccuracy and added additional output. Changes in version 1.5.6: o Added function minorAlleleSensitivitySpecificity. Changes in version 1.5.5: o Deprecated pedigreeClean and pedigreeFindDuplicates. pedigreeCheck now encompasses all pedigree checks and should be used instead. o Added pedigreeMaxUnrelated to find the maximum set of unrelated members of a pedigree. o Added additional output column "MAF" to matrix returned by alleleFrequency. Changes in version 1.5.4: o Removed hard-coding of autosomes as 1:22; can now set a vector of integer codes corresponding to autosomes with "autosomeCode" argument at object creation and retrieve with "autosomeCode" methods. This change makes GWASTools compatible with non-human organisms. o Added option to duplicateDiscordanceAcrossDatasets to count missing data as discordance. o Added option to start axes of genoClusterPlot at 0. Changes in version 1.5.3: o Removed "alleleA.col" and "alleleB.col" options from plink functions, as "alleleA" and "alleleB" are now standard names. o Added "getAlleleA" and "getAlleleB" methods to GdsGenotypeReader. o Added "getDimension" method to NcdfReader. Changes in version 1.5.2: o Added "getAlleleA" and "getAlleleB" methods to SnpAnnotation* and GenotypeData objects. o Added genotypeToCharacter function to convert genotypes from number of A alleles to A/B format. o getGenotype for GenotypeData has option char=TRUE to return character genotypes in A/B format. Changes in version 1.5.1: o Added option to duplicateDiscordanceAcrossDatasets to calculate minor allele discordance. Changes in version 1.3.16: o Added convertVcfGds to extract bi-allelic SNPs from a VCF file. o Added ncdfImputedDosage to convert output from common imputation programs to NetCDF. assocTestRegression has an additional argument dosage=TRUE to be used with these files. o Added vignette describing GWASTools data structures. Changes in version 1.3.15: o Bug fix in pedigreePairwiseRelatedness related to use of character identifiers. Changes in version 1.3.14: o assocTestRegression returns NA for snps where cases or controls are monomorphic, added assocTestFisherExact to use in that case. o Added snp.exclude argument to pseudoautoIntensityPlot. o Bug fix in messages reporting file read times when creating or checking netCDF files. Changes in version 1.3.13: o Added vignette on converting VCF to NetCDF with annotation. o Prevent duplicateDiscordance from checking correlation by SNP in cases of no variation. Changes in version 1.3.12: o Added GdsReader and GdsGenotypeReader classes with dependency on gdsfmt. GenotypeData objects can also be created with GdsGenotypeReader objects in the "data" slot. Changes in version 1.3.11: o Fixed bug in duplicateDiscordance when Y chromosome is not included. Changes in version 1.3.10: o Fixed bug in chromIntensityPlot so ideogram scales correctly if SNPs are excluded. Changes in version 1.3.9: o Fixed bug in assocTestCPH that could lead to false positives if additive model failed but GxE model did not. o Allow multiple variables for stratified analysis in assocTestCPH. Changes in version 1.3.8: o Pedigree functions accept non-numeric identifiers and provide additional output. Changes in version 1.3.7: o In batchChisqTest, Yates correction cannot be bigger than the terms it corrects. Changed to match bug fix to chisq.test in R 2.15.1. Changes in version 1.3.6: o Removed automatic subtitle from qqPlot. o Allow selection of theoretical boundaries to draw in ibdPlot. Changes in version 1.3.5: o Added function asSnpMatrix to convert a GenotypeData object to a SnpMatrix object for use with snpStats. Changes in version 1.3.4: o Added chromosome ideograms to chromIntensityPlot and anomStatsPlot. anomStatsPlot has an option to put multiple anomalies on the same plot. Changes in version 1.3.3: o Updated vignette. Changes in version 1.3.2: o Use lazy loading of data. o manhattanPlot and snpCorrelationPlot accept character vectors of chromosome; chrom.labels argument no longer used. Changes in version 1.3.1: o close method of NcdfReader returns invisibly. Changes in version 1.1.9: o anomSegStats checks for SNPs in centromere gaps. o anomStatsPlot has option to plot LRR/BAF individually (for greater flexibility in layout). o Updates to arguments for plot titles in chromIntensityPlot, anomStatsPlot, and pseudoautoIntensityPlot for consistency. o plinkCheck has map.alt argument to override default GenotypeData -> PLINK annotation conversion. Changes in version 1.1.8: o Updated positions of pseudoautosomal regions. o Added plinkToNcdf to convert PLINK files to NetCDF for use in GWASTools. Changes in version 1.1.7: o chromIntensityPlot and pseudoautoIntensityPlot have cex=0.5 by default. o chromIntensityPlot colors now match anomStatsPlot colors. o plinkCheck has options to skip checking parents and sex. o plinkCheck sorts alleles by character to avoid phase mismatches. o plinkWrite and plinkCheck print progress messages if verbose=TRUE. Changes in version 1.1.6: o duplicateDiscordance and duplicateDiscordanceAcrossDatasets use only one pair of scans per subject by default. o duplicateDiscordanceProbability sets small negative values to 0. Changes in version 1.1.5: o duplicateDiscordance has an option to compute correlation by SNP. o Added scan.exclude argument to plinkCheck. Changes in version 1.1.4: o Added ncdfSetMissingGenotypes function. o plinkCheck now writes a log file with all mismatches found. o duplicateDiscordance excludes Y chrom SNPs for females. o duplicateDiscordance has an option to consider only pairs involving the minor allele. Changes in version 1.1.3: o batchChisqTest and batchFisherTest now return n results for n batches even if n=2. o batchFisherTest has return.by.snp=FALSE as default. Changes in version 1.1.2: o Added LR tests to assocTestRegression. o Bug fix in calculation of mean odds ratio in batchFisherTest. o Bug fix in missingGenotypeByScanChrom for data sets with only one female. Changes in version 1.1.1: o Added functions plinkWrite and plinkCheck for writing and checking PLINK ped and map files. o Added pcaSnpFilters data set for identifying regions with high PC-SNP correlation.