R/dataset_docum.R

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

#' example gds file used in vignette.
#'
#' This gds file contains genotype and phenotype for 92 whole-genome
#' sequenced samples captured by CCDS region.  This is a merged
#' dataset of the 87 benchmark samples and the 5 study samples (all
#' are assembled from the 1000 Genomes Project).  The meta info for
#' these 92 samples includes sample name, pupulation, age, relation
#' note and group info (benchmark or study).
#'
#' @name example.gds
#' @docType data
#' @author Qian Liu \email{qliu7@@buffalo.edu}
#' @keywords datasets
NULL

#' Example vcf file used in vignette.
#'
#' This vcf file contains only a subset (1000 lines of variants) of
#' the original vcf file for the 5 study samples (examples assembled
#' from the 1000 Genomes Project).  This is to be used as a runnable
#' example in the function of \code{LoadVfile} and \code{sampleQC} in
#' the vignette.
#'
#' @name example_sub.vcf
#' @docType data
#' @author Qian Liu \email{qliu7@@buffalo.edu}
#' @keywords datasets
NULL

#' Example capture region file used in vignette.
#'
#' This \code{.bed} file contains only CCDS capture region only in
#' chromosome 1, which is meant to be used together with the
#' \code{example_sub.vcf} as a runnable example in the function of
#' \code{LoadVfile} and \code{sampleQC} in the vignette.
#'
#' @name CCDS.Hs37.3.reduced_chr1.bed
#' @docType data
#' @author Qian Liu \email{qliu7@@buffalo.edu}
#' @keywords datasets
NULL

#' Example SeqSQC file used in vignette.
#'
#' The SeqSQC object is a list of two objects. The first object
#' \code{gdsfile} is the filepath of the "example.gds" file which
#' stores the genotype and meta info of the example data merged with
#' the benchmark data.  The second object \code{QCresult} contains the
#' data dimensions (# of samples and variants), sample annotation, and
#' QC results for sample missing rate, sex check, inbreeding outlier
#' check, IBD check, and population outlier check.
#' @name example.seqfile.Rdata
#' @docType data
#' @author Qian Liu \email{qliu7@@buffalo.edu}
#' @keywords datasets
NULL

#' Sample annotation file for the example data used in vignette.
#'
#' This sample annotation file is a required input from the user when
#' using SeqSQC.  It includes the sample info with sample name stored
#' in the column of \code{sample}, the population info stored in the
#' column of \code{population}, and the gender info stored in the
#' column of \code{gender}.  The \code{population} column must be a in
#' the format of "AFR/EUR/ASN/EAS/SAS". The \code{gender} column must
#' be in the format of "female/male". This file is meant to be used
#' together with the \code{example_sub.vcf} as a runnable example in
#' the function of \code{LoadVfile} and \code{sampleQC} in the
#' vignette.
#' @name sampleAnnotation.txt
#' @docType data
#' @author Qian Liu \email{qliu7@@buffalo.edu}
#' @keywords datasets
NULL