# A bioconductor package for sample quality check with next generation sequencing data

## Documentation for package ‘SeqSQC’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

SeqSQC-package | Sample Quality Check for NGS Data using SeqSQC package
"gdsfile<-"-method | A data format to store genotype phenotype and sample QC results from SeqSQC.
"QCresult<-"-method | A data format to store genotype phenotype and sample QC results from SeqSQC.
CCDS.Hs37.3.reduced_chr1.bed | Example capture region file used in vignette.
example.gds | example gds file used in vignette.
example.seqfile.Rdata | Example SeqSQC file used in vignette.
example_sub.vcf | Example vcf file used in vignette.
gdsfile | A data format to store genotype phenotype and sample QC results from SeqSQC.
gdsfile-method | A data format to store genotype phenotype and sample QC results from SeqSQC.
gdsfile<- | A data format to store genotype phenotype and sample QC results from SeqSQC.
gdsfile<--method | A data format to store genotype phenotype and sample QC results from SeqSQC.
IBDCheck | Sample relationship check with SeqSQC object input file.
IBDRemove | Obtain the problematic sample list from IBD relatedness.
Inbreeding | Sample inbreeding check with SeqSQC object input file.
LoadVfile | Data preprocessing for VCF or plink input from NGS or GWAS data.
MissingRate | Sample missing rate check with SeqSQC object input file.
PCACheck | Population outlier check with SeqSQC object input file.
plotQC | Plot the QC results for specific QC steps.
problemList | Generate the problematic sample list.
QCresult | A data format to store genotype phenotype and sample QC results from SeqSQC.
QCresult-method | A data format to store genotype phenotype and sample QC results from SeqSQC.
QCresult<- | A data format to store genotype phenotype and sample QC results from SeqSQC.
QCresult<--method | A data format to store genotype phenotype and sample QC results from SeqSQC.
RenderReport | Render the rmarkdown file for generating a sample QC report.
sampleAnnotation.txt | Sample annotation file for the example data used in vignette.
sampleQC | The wrap-up function for sample QC of sequencing/GWAS data.
SeqOpen | Open the gds file in SeqSQC objects.
SeqSQC | A data format to store genotype phenotype and sample QC results from SeqSQC.
SeqSQC-class | A data format to store genotype phenotype and sample QC results from SeqSQC.
SexCheck | Sample gender check with SeqSQC object input file.