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

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Documentation for package ‘SeqSQC’ version 1.22.0

• 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.