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#' A list of phenotype data.frames
#'
#' A list of four phenotype data frames used throughput the package.
#'
#' @name pd
#' @docType data
#' @format A list of four data.frames:
#' \describe{
#' \item{Sep }{ phenotype information for samples from
#' <https://www.biorxiv.org/content/10.1101/567966v1>; a data.frame with
#' 23 rows and 15 columns. Column descriptions: SampleID is the sample name,
#' Zone is the RNA fraction of the sample ("Nucleus" or "Cytosol"), Age,
#' Sex, and Race list these demographic characteristics, Fetal categorizes
#' each sample age as "Fetal" or "Adult", Library categorizes the RNAseq
#' library preparation method as polyA selection ("polyA") or rRNA depletion
#' ("RiboZero"), RIN_fraction is the RNA Integrity Number for each sample,
#' sumMapped is the number of mapped reads, Shortlabels, Label, col, and
#' LabelFrac are columns of information for plotting, BigWig is the name of
#' the BigWig file for each sample, and files lists the URL for the BigWig
#' online.}
#' \item{Deg }{ phenotype information for samples from
#' <https://www.pnas.org/content/114/27/7130>; a data.frame with 40 rows
#' and 16 columns. Column descriptions: DegradationTime is the number of minutes
#' the brain tissue for each sample was left on the benchtop at room
#' temperature before RNA was extracted, AgeDeath is the age of the donor
#' at time of death, Dx lists whether the donor was diagnosed as
#' schizophrenic or was a neurotypical control, Sex and Race list these
#' demographic characteristics for each sample, pH lists the pH of the
#' brain at collection, PMI is the postmortem interval between death and
#' brain harvesting, BrNum is the donor number, RIN is the RNA Integrity
#' Number for the RNA sample, LibraryProtocol categorizes the RNAseq
#' library preparation method as polyA selection ("polyA") or rRNA
#' depletion ("Ribo"), SampleID is the ID for the sample, totalAssignedGene
#' is the proportion of reads mapping to a gene body, sumMapped is the
#' number of mapped reads, BigWig is the name of the BigWig file,
#' SampleID_library is the Sample ID and library column values together,
#' and files lists the URL for the BigWig online.}
#' \item{Cell }{ phenotype information for samples from
#' <https://www.pnas.org/content/112/23/7285>; a data.frame with 466
#' rows and 11 columns. Column descriptions: geo_accession is the accession
#' number for each sample in the Gene Expression Omnibus, Age is the numeric
#' age of each sample, AgeGroup categorizes each sample age as "prenatal"
#' or "postnatal", sub_tissue lists whether the sample was from cortex or
#' hippocampus, Cluster_color is the color for each sample for plotting,
#' Cell_type is the cell identity assigned to each sample, RunName is the
#' run name assigned to each sample in the Sequence Read Archive (SRA),
#' SubjectID is the subject label, sumMapped is the number of mapped reads,
#' BigWig is the name of the BigWig file, and files lists the URL for the
#' BigWig online.}
#' \item{Sort }{ phenotype information for samples from
#' <https://www.biorxiv.org/content/10.1101/428391v2>; a data.frame with
#' 12 rows and 12 columns. Column descriptions: Description categorizes the
#' RNAseq library preparation method as polyA selection ("PolyA") or rRNA
#' depletion ("Ribo"), SubjectID is the subject number, CellType lists
#' whether the sample was labeled by NeuN antibody (neuronal, "NeuN_Plus")
#' or not (non-neuronal, "NeuN_Minus"), SampleID combines the sample number,
#' cell type and library of each sample in one column, BrNum is the donor
#' ID, RIN is the RNA Integrity Number for each RNA sample, Age is the
#' numeric age at death, sumMapped is the number of mapped reads, Label and
#' col provide information for plotting, BigWig is the name of each BigWig
#' file, and files lists the URL for the BigWig online.}
#' }
#'
#' @keywords datasets
#' @seealso [four_panels] [brainflowprobes_cov]
#' <https://github.com/LieberInstitute/brainflowprobes/blob/master/data-raw/create_sysdata.R>
#' @examples
#' ## pd <- list(Sep = pdSep, Deg = pdDeg, Cell = pdCell, Sort = pdSort)
NULL
#' Example base-pair region coverage data
#'
#' A list of base-pair region coverage data.frame lists used for exemplifying
#' the package functionality. This is the data extracted for the example region
#' `chr20:10286777-10288069:+` by looping through the phenotype tables
#' stored in `pd` and using the
#' [getRegionCoverage][derfinder::getRegionCoverage] function. This can be
#' reproduced using the [brainflowprobes_cov] function in this package.
#'
#' @name four_panels_example_cov
#' @docType data
#' @format A list with the base-pair coverage output from
#' [brainflowprobes_cov] with the example region used throughout the
#' package documentation ('chr20:10286777-10288069:+').
#' \describe{
#' \item{Sep }{ base-pair coverage region data.frame list for pd$Sep,}
#' \item{Deg }{ base-pair coverage region data.frame list for pd$Deg,}
#' \item{Cell }{ base-pair coverage region data.frame list for pd$Cell,}
#' \item{Sort }{ base-pair coverage region data.frame list for pd$Sort.}
#' }
#'
#' @keywords datasets
#' @seealso [four_panels] [plot_coverage]
#' @examples
#' if (FALSE) {
#' ## Takes about 10 minutes to run!
#' four_panels_example_cov <- brainflowprobes_cov(
#' "chr20:10286777-10288069:+"
#' )
#' }
NULL
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