NEWS
SeqSQC 0.99.11
- update the 'sampleQCReport.Rmd' with 'warning=FALSE' for interactive plotting.
- add default values for 'plotQC(QCstep=c())'.
SeqSQC 0.99.10
- updated the man for 'sampleQC' and 'LoadVfile'.
SeqSQC 0.99.9
- Updated the 'output' argument in function of 'sampleQC' and 'LoadVfile', by using the default value of 'sampleqc' in working directory. In vignette and the example code of these 2 functions, temporary directory is used for the directory to save the QC results.
SeqSQC 0.99.8
- vignette, using a tempdir() for vignette output.
- Vignette: Additional explanation added for the option to do a wrapper all-inclusive QC or specific QC steps.
- documentation for argument "output" in "LoadVfile" and "sampleQC", to indicate that the 'dirname(output)' would be used as the directory to save the other QC results in '.txt' and plots in '.pdf'. The default value is added as '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.
SeqSQC 0.99.7
- Added checking for input in subsetGDS.
- Removed commented code for subsetGDS.
- SeqSQCclass renamed as SeqSQC.
- mergeGDS.R. using lapply for some repeated functions like "read.gdsn(index.gdsn())". In SexCheck, Inbreeding, IBDCheck, PCACheck.
- sampleQC: 1. check the class of vfile for SeqSQC file or vcf/plink file, instead of using vfile / sfile.
- plotting function writing separately (not export), wrapper with plotQC().
- Removed IBDRemoveAll.R. Will check IBD for all sample pairs (including benchmark samples) by adding argument "all" in "IBDRemove.R".
- debugged warning messages from "LoadVfile" and using "rbokeh".
SeqSQC 0.99.6
- modified SeqSQCclass to SeqSQC (not in vignette..).
SeqSQC 0.99.5
- Installed BiocGenerics locally.
SeqSQC 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