LoadVfile: Data preprocessing for VCF or plink input from NGS or GWAS...

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

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)

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