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

In SeqSQC: A bioconductor package for sample quality check with next generation sequencing 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 [e-mail]

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)

SeqSQC documentation built on Nov. 8, 2020, 5:03 p.m.