transfer from atarca

DESCRIPTION

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+Package: pregnomics
+Type: Package
+Title: Data package for the study: Targeted expression profiling by RNA-Seq improves detection of cellular dynamics during pregnancy and identifies a role for T cells in term parturition
+Version: 1.0
+Date: 2018-11-29
+Author: Adi L Tarca
+Maintainer: Adi L Tarca <[email protected]>
+Description: Inlcudes gene expression data obtained with four platforms for 32 blood samples as well as relevant metadata for samples, genes, and gene sets relevant to the study.
+License: MIT + file LICENSE
+RoxygenNote: 6.1.1

LICENSE

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+MIT License
+
+Copyright (c) 2018 atarca
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

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+exportPattern("^[[:alpha:]]+")

R/data.R

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+#' Annotation data for samples
+#' A dataset containing the annotation of 32 maternal blood samples
+#' @format A data frame with 32 rows and 8 variables:
+#' \describe{
+#'   \item{SampleID}{Unique sample identifier}
+#'   \item{IndividualID}{Individual ID}
+#'   \item{GA}{Gestational Age, in weeks}
+#'   \item{Group}{Labor Group: TIL term in labor; TNL term not in labor}
+#'   \item{RIN}{RNA Integrity Number }
+#'   \item{StorageMonths}{Sample storage duration from collection to analysis in months}
+#'   \item{GAAnalysis}{Sample was used in the GA effect analysis}
+#'   \item{LaborAnalysis}{Sample was used in the labor effect analysis}
+#' }
+#' @source \url{}
+"ano32"
+
+#'Gene expression matrix obtained with Affymetrix HTA 2.0 arrays
+#' HTA gene expression for 32 maternal blood samples
+#' @format A matrix with RMA log2 expression summaries
+#' \describe{
+#' rows are transcript cluster IDs and columns are samples matching rows in ano32
+#' }
+#' @source \url{}
+"esetHTA"
+
+
+#'Gene expression matrix obtained with qRT-PCR
+#' qRT-PCR gene expression for 32 maternal blood samples
+#' @format A matrix with -Delta CT values
+#' \describe{
+#' rows are gene symbols and columns are samples matching rows in ano32
+#' }
+#' @source \url{}
+"esetPCR"
+
+#'Gene expression count matrix obtained with RNASeq
+#' Salmon quantified gene expression for 32 maternal blood samples
+#' @format A matrix of counts of sequencing fragments
+#' \describe{
+#' rows are ENSEMBLE gene identifiers and columns are samples matching rows in ano32
+#' }
+#' @source \url{}
+"Rcount"
+
+
+#'Gene expression count matrix obtained with DriverMap (Cellecta Inc)
+#' Salmon quantified gene expression for 32 maternal blood samples
+#' @format A matrix of counts of sequencing fragments
+#' \describe{
+#' rows are ENSEMBLE gene identifiers and columns are samples matching rows in ano32
+#' }
+#' @source \url{}
+"Ccount"
+
+
+#' Single cell transcripomics gene signatures
+#' A dataset containing the genes specifically expressed in different type of cells from the 
+#' paper PMID: 28830992
+#' @format A data frame with 32 rows and 8 variables:
+#' \describe{
+#'   \item{Symbol}{Gene Symbol}
+#'   \item{Type}{Cell type}
+#' }
+#' @source \url{}
+"SCGeneSets"
+
+
+#' Top table of changes with gestation in maternal blood by Al-Grawi et al.
+#' A dataset containing the genes specifically expressed in different type of cells from the 
+#' paper PMID: 27711190
+#' @format A data frame with 32 rows and 8 variables:
+#' \describe{
+#'   \item{ID}{Illumina probe ID}
+#'   \item{adj.P.Val}{Adjusted p-value}
+#'  \item{logFC}{log2 fold change betwene late and early gestation}
+#'   \item{P.Value}{Nominal p-value}
+#'   \item{Gene.symbol}{Gene symbol}
+#' }
+#' @source \url{}
+"algarawi"
+
+
+#' Top table of changes with gestation in maternal blood by Heng et al.
+#' A dataset containing the genes specifically expressed in different type of cells from the 
+#' paper PMID: 27333071
+#' @format A data frame with 32 rows and 8 variables:
+#' \describe{
+#'   \item{SYMBOL}{Gene symbol}
+#'   \item{logFC}{log2 fold change betwene late and early gestation}
+#'   \item{P.Value}{Nominal p-value}
+#'   \item{adj.P.Val}{Adjusted p-value}
+#'   \item{Gene.symbol}{Gene symbol}
+#' }
+#' @source \url{}
+"heng"
+
+
+#' Number of expressed exon level probesets per transcript cluster
+#' Obtained based on detection above background p-values from TAC from cell files corresponding to esetHTA
+#' @format A data frame with 32 rows and 8 variables:
+#' \describe{
+#'   \item{npspge}{number of probesets expressed above background in 5 or more of the 32 samples. Names are transcript cluster IDS}
+#' }
+#' @source \url{}
+"npspge"
+
+
+