R/data.R

In LieberInstitute/brainstorm: Validating Sample Identiy Through RNA-seq and DNA Genotyping Correlation

#' Test SNP matrix
#'
#' A test SNP input `matrix`.
#'
#' @format A `matrix` with zeros and ones representing the genotypes.
#' @source <https://github.com/LieberInstitute/brainstorm/blob/master/data-raw/test_snps.R>
"test_snps"

#' Test brain donor table
#'
#' A test `data.frame` with example data for samples with brain donor ids (BrNums).
#'
#' @format A `data.frame` with two columns: `Sample` and `BrNum`.
#' @source <https://github.com/LieberInstitute/brainstorm/blob/master/data-raw/test_BrTable.R>
"test_BrTable"

#'Example Genotype Data
#'
#'TOPMed Genotype data (746 snps) for the 42 samples in brain_sentrix
#'
#'@format `CollapsedVCF`
#'@source \url{https://github.com/LieberInstitute/SPEAQeasy-example}
"snpsGeno_VCF"

#' Brain Sentrix Table
#'
#' Genotype sample sheet for 42 samples from 39 unique brains
#'
#'@format `data.frame`
#'@source \url{https://github.com/LieberInstitute/SPEAQeasy-example}
"brain_sentrix"

#' Example RNA snps (imputed Genotypes)
#'
#'Imputed snps from RNA data, 665 snps for 42 samples
#'@format `CollapsedVCF`
#'@source \url{https://github.com/LieberInstitute/SPEAQeasy-example}
"snpsCalled_VCF"

#'Example Phenotype Table
#'
#'Phenotype data for 42 samples
#'
#'@format `data.frame`
#'@source \url{https://github.com/LieberInstitute/SPEAQeasy-example}
"pd_example"