Man pages for SeqSQC
A bioconductor package for sample quality check with next generation sequencing data

CCDS.Hs37.3.reduced_chr1.bedExample capture region file used in vignette.
example.gdsexample gds file used in vignette.
example.seqfile.RdataExample SeqSQC file used in vignette.
example_sub.vcfExample vcf file used in vignette.
IBDCheckSample relationship check with SeqSQC object input file.
IBDRemoveObtain the problematic sample list from IBD relatedness.
InbreedingSample inbreeding check with SeqSQC object input file.
LoadVfileData preprocessing for VCF or plink input from NGS or GWAS...
MissingRateSample missing rate check with SeqSQC object input file.
PCACheckPopulation outlier check with SeqSQC object input file.
plotQCPlot the QC results for specific QC steps.
problemListGenerate the problematic sample list.
RenderReportRender the rmarkdown file for generating a sample QC report.
sampleAnnotation.txtSample annotation file for the example data used in vignette.
sampleQCThe wrap-up function for sample QC of sequencing/GWAS data.
SeqOpenOpen the gds file in SeqSQC objects.
SeqSQC-classA data format to store genotype phenotype and sample QC...
SeqSQC-packageSample Quality Check for NGS Data using SeqSQC package
SexCheckSample gender check with SeqSQC object input file.
SeqSQC documentation built on April 29, 2020, 3:28 a.m.