SeqSQC-class: A data format to store genotype phenotype and sample QC...

In SeqSQC: A bioconductor package for sample quality check with next generation sequencing data

Description

A SeqSQC object is a list of two objects. The first object gdsfile is the filepath of the GDS (discussed in section below) file which stores the genotype information from the original VCF file. The second object QCresult is a list of sample information and QC results, which include the dimension (# of samples and variants), sample annotation, and QC results for sample missing rate, sex check, inbreeding outlier check, IBD check, and population outlier check.

Usage

SeqSQC(gdsfile, QCresult = List())

gdsfile(x)

gdsfile(x) <- value

QCresult(x)

QCresult(x) <- value

## S4 method for signature 'SeqSQC'
gdsfile(x)

## S4 replacement method for signature 'SeqSQC'
gdsfile(x) <- value

## S4 method for signature 'SeqSQC'
QCresult(x)

## S4 replacement method for signature 'SeqSQC'
QCresult(x) <- value

Arguments

gdsfile	A character string for the filepath of the GDS file.
QCresult	A list with sample information and sample QC results.
x	an SeqSQCClass object.
value	the new value for the SeqSQC object slots.

Value

The filepath to the gds file.

Slots

gdsfile

A character string for the filepath of the GDS file.

QCresult

A list with sample information and sample QC results.

Examples

load(system.file("extdata", "example.seqfile.Rdata", package="SeqSQC"))
gdsfile(seqfile)
QCresult(seqfile)

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