Man pages for Liubuntu/SeqSQC
A bioconductor package for sample quality check with next generation sequencing data
| 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. |
| 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... |
| 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. |
| 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-class | A data format to store genotype phenotype and sample QC... |
| SeqSQC-package | Sample Quality Check for NGS Data using SeqSQC package |
| SexCheck | Sample gender check with SeqSQC object input file. |
