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

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Documentation for package ‘SeqSQC’ version 1.9.1

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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.