Description Usage Arguments Details Value Author(s) Examples
Function to read VCF or plink files, merge with benchmark data, and output as SeqSQC object.
1 2 3 4 |
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 |
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
|
format.data |
the data source. The default is |
format.file |
the data format. The default is |
... |
Arguments to be passed to other methods. |
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".
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.
Qian Liu qliu7@buffalo.edu
1 2 3 4 5 6 | 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)
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