LoadVfile {SeqSQC} | R Documentation

## Data preprocessing for VCF or plink input from NGS or GWAS data.

### Description

Function to read VCF or plink files, merge with benchmark data, and output as SeqSQC object.

### Usage

    LoadVfile(vfile, 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", ...)

### Arguments

`vfile` | vcf or PLINK input file (ped/map/bed/bim/fam with same basename). Vfile could be a vector of character strings, see details.
`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 results and plots. The default is `sampleqc` in 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`.
`...` | Arguments to be passed to other methods.

### Details

For `vfile` with more than one file names, `LoadVfile` 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.
`sample.annot` file contains 3 columns with column names. 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.

### Author(s)

Qian Liu qliu7@buffalo.edu

### Examples

    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 <- LoadVfile(vfile = infile, output = outfile, capture.region = cr,
    sample.annot = sample.annot)

[Package SeqSQC version 1.12.0 Index]