0.99.11改变版本 ---------------------------- - 更新“sampleQCReport。Rmd '与'警告=FALSE '的交互式绘图。—为' plotQC(QCstep=c()) '添加默认值。0.99.10改变版本 ---------------------------- - 更新的人“sampleQC”和“LoadVfile”。更改版本0.99.9 ---------------------------- -更新'输出'参数的功能' sampleQC '和' LoadVfile '，通过使用' sampleQC '的默认值在工作目录。在小插图和这两个函数的示例代码中，保存QC结果的目录使用临时目录。0.99.8改变版本 ---------------------------- - 为装饰图案装饰图案,使用tempdir()输出。-小插图:增加了对包装器全包QC或特定QC步骤的选项的额外解释。-“LoadVfile”和“sampleQC”中参数“output”的文档，以表明“dirname(output)”将被用作保存“.txt”中其他QC结果和“.pdf”中绘图的目录。默认值添加为' file.path(tempdir()， "sampleqc") '。——sampleQC。R: Arguments of `plotting=TRUE, results=TRUE` added and documented, giving the option for users to whether or not output the QC results and plots. The problem list will always in output for the simplest sample QC result and summary. - the package documentation updated, by adding a `@seealso` for links of main functions of SeqSQC. CHANGE IN VERSION 0.99.7 ---------------------------- o Added checking for input in subsetGDS. o Removed commented code for subsetGDS. o SeqSQCclass renamed as SeqSQC. o mergeGDS.R. using lapply for some repeated functions like "read.gdsn(index.gdsn())". In SexCheck, Inbreeding, IBDCheck, PCACheck. o sampleQC: 1. check the class of vfile for SeqSQC file or vcf/plink file, instead of using vfile / sfile. o plotting function writing separately (not export), wrapper with plotQC(). o Removed IBDRemoveAll.R. Will check IBD for all sample pairs (including benchmark samples) by adding argument "all" in "IBDRemove.R". o debugged warning messages from "LoadVfile" and using "rbokeh". CHANGE IN VERSION 0.99.6 ---------------------------- o modified SeqSQCclass to SeqSQC (not in vignette..). CHANGE IN VERSION 0.99.5 ---------------------------- o Installed BiocGenerics locally. CHANGE IN VERSION 0.99.4 ---------------------------- Load benchmark data from ExperimentHub o added in the R script, will download only once with first time running of the LoadVfile() or sampleQC(). Bioconductor submission check: o Added unit test. o Added a NEWS file to keep track of changes o Added zzz.R to fix the no visible binding for global functions or variables. o Added the "example_sub.vcf" for 1000 lines of variants to run as example in the package vignette. o Added accessor methods for SeqSQCclass data structure to get the slots of "gdsfile" and "QCresult". Vignettes: o Added bioconductor installation and library load section in the vignette. o Added runnable example vcf file added in "inst/extdata/example_sub.vcf", with 1000 lines of variants. MAN: o added package documentation for dataset, class, methods and constructor.