sampleQC {SeqSQC} | R Documentation

## The wrap-up function for sample QC of sequencing/GWAS data.

### Description

A wrap-up function for sample QC. It reads in the variant genotypes in vcf/PLINK format, merges study cohort with benchmark data, and performs sample QC for the merged dataset.

### Usage

    sampleQC(vfile = NULL, output = "sampleqc", capture.region = NULL,
      sample.annot = NULL, LDprune = TRUE, vfile.restrict = FALSE,
      slide.max.bp = 5e+05, ld.threshold = 0.3, format.data = "NGS",
      format.file = "vcf", QCreport = TRUE, out.report = "report.html",
      interactive = TRUE, results = TRUE, plotting = TRUE, ...)

### Arguments

`vfile` | vcf or PLINK input file (ped/map/bed/bim/fam with same basename). The default is NULL. Vfile could be a vector of character strings, see details. Could also take file in `SeqSQC` object generated from `LoadVfile`.
`output` | a character string for name of merged data of SeqSQC object. The `dirname(output)` would be used as the directory to save the QC result and plots. The default is `sampleqc` in the working directory.
`capture.region` | the BED file of sequencing capture regions. The default is NULL. For exome-sequencing data, the capture region file must be provided.
`sample.annot` | sample annotation file with 3 columns (with header) in the order of sample id, sample population and sex info. The default is NULL.
`LDprune` | whether to use LD-pruned snp set. The default is TRUE.
`vfile.restrict` | whether the input vcf or plink file has already been restricted by capture region. The default is FALSE.
`slide.max.bp` | the window size of SNPs when calculating linkage disequilibrium. The default is 5e+05.
`ld.threshold` | the r^2 threshold for LD-based SNP pruning if `LDprune = TRUE`. The default is 0.3.
`format.data` | the data source. The default is `NGS` for sequencing data.
`format.file` | the data format. The default is `vcf`.
`QCreport` | Whether to generate the sample QC report in html format.
`out.report` | the file name for the sample QC report. The default is `report.html`.
`interactive` | whether to generate interactive plots in the sample QC report if `QCreport = TRUE`.
`results` | whether to write out the results for each QC steps in .txt files. The default is TRUE.
`plotting` | whether to output the plots for each QC steps in .pdf files. the default is TRUE.
`...` | Arguments to be passed to other methods.

### Details

For `vfile` with more than one file names, `sampleQC` will merge all dataset together if they all contain the same samples. It is useful to combine genetic/genomic data together if VCF data is divided by chromosomes.
There are 3 columns in `sample.annot` file. col 1 is `sample` with sample ids, col 2 is `population` with values of "AFR/EUR/ASN/EAS/SAS", col 3 is `gender` with values of "male/female".

### Value

a SeqSQC object with the filepath to the gds file which stores the genotype, the summary of samples and variants, and the QCresults including the sample annotation information and all QC results.

### Author(s)

Qian Liu qliu7@buffalo.edu

### Examples

    ## Not run:
    infile <- system.file("extdata", "example_sub.vcf", package="SeqSQC")
    sample.annot <- system.file("extdata", "sampleAnnotation.txt", package="SeqSQC")
    cr <- system.file("extdata", "CCDS.Hs37.3.reduced_chr1.bed", package="SeqSQC")
    outfile <- file.path(tempdir(), "testWrapUp")
    seqfile <- sampleQC(vfile = infile, output = outfile, capture.region = cr,
    sample.annot = sample.annot, format.data = "NGS", format.file = "vcf",
    QCreport = TRUE, out.report="report.html", interactive = TRUE)
    ## save(seqfile, file="seqfile.RData")

    load(system.file("extdata", "example.seqfile.Rdata", package="SeqSQC"))
    gfile <- system.file("extdata", "example.gds", package="SeqSQC")
    seqfile <- SeqSQC(gdsfile = gfile, QCresult = QCresult(seqfile))
    seqfile <- sampleQC(sfile = seqfile, output = outfile, QCreport = FALSE,
    out.report="report.html", interactive = TRUE)

    ## End(Not run)

[Package SeqSQC version 1.12.0 Index]