SeqSQC-package |
Sample Quality Check for NGS Data using SeqSQC package |
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. |
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. |
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. |