R/datasets.R

#' @name uc_crohns_rawData.RData
#' @title uc_crohns_rawData.RData
#' @docType data
#' @source http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36807
#' @details Used getGEO to get data on January 13, 2014
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#' @name cucRomer.RData
#' @title cucRomer.RData
#' @docType data
#' @source generated by the UC vs Crohn's analysis vignette
#' @details used \code{limma} \code{romer} to generate results
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#' @name skin_rma_data.RData
#' @title skin_rma_data.RData
#' @docType data
#' @source generated using raw data files from Jeffrey Petruska.
#' @details RMA normalized Affymetrix data.
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#' @name muscle_data.RData
#' @title muscle_data.RData
#' @docType data
#' @source http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4411
#' @details RMA normalized intensities downloaded from GEO using \code{getGEO}, on January 13, 2014; data was trimmed down to only the denervated and innervated controls
NULL


#' @name skinRomer.RData
#' @title skinRomer.RData
#' @docType data
#' @source running \code{romer} on skin t7 vs t0 and t14 vs t0 comparisons
#' @details did two sets of contrasts, t7 vs t0 and t14 vs t0 using the \code{multicontrastRomer} function
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#' @name skinGeneSetTest.RData
#' @title skinGeneSetTest.RData
#' @docType data
#' @source running \code{geneSetTest} on skin t7 vs t0 and t14 vs t0 comparisons
#' @details did two sets of contrasts, t7 vs t0 and t14 vs t0, and up, down, and mixed alternative tests using \code{mmGeneSetTest}
NULL

#' @name muscleRomer.RData
#' @title muscleRomer.RData
#' @docType data
#' @source running \code{romer} on muscle denervated over innervated
#' @details did one contrast, denervated vs innervated using the \code{multicontrastRomer} function
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#' @name muscleGeneSetTest.RData
#' @title muscleGeneSetTest.RData
#' @docType data
#' @source running \code{mmGeneSetTest} on muscle denervated over innervated
#' @details did one contrast, denervated vs innervated using the \code{mmGeneSetTest} function
NULL


#' @name cucCCOutput.RData
#' @title cucCCOutput.RData
#' @docType data
#' @source interacting with GO nodes in Cytoscape to partition into groups
#' @details After performing \code{ccCompare} on \code{cucRomer}, any edges =< 0.8 similarity were removed, and the graph loaded into Cytoscape using \code{ccOutCyt}. Individual groups of GO nodes were determined by Robert M Flight visualy and exploratively, and labels assigned based on biological knowledge of Robert M Flight. Each GO group is defined in \code{cucNodeGroups}, with the list of GO terms that are part of that group, along with their attributes.
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#' @name skinMuscleCCOutput.RData
#' @title skinMuscleCCOutput.RData
#' @docType data
#' @source interacting with GO nodes in Cytoscape to partition into groups
#' @details After performing \code{ccCompare} on \code{allCCRomer}, any edges =< 0.8 similarity were removed, and the graph loaded into Cytoscape using \code{ccOutCyt}. Individual groups of GO nodes were determined by Robert M Flight visualy and exploratively, and labels assigned based on biological knowledge of Robert M Flight. Each GO group is defined in \code{smNodes}, with the list of GO terms that are part of that group, along with their attributes.
NULL
rmflight/ccPaper documentation built on May 25, 2017, 4:26 a.m.