Found 32698 results in 8825 files, showing top 50 files (show more).
XVector:R/RdsCollection-class.R: [ ] |
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45: .validate_dirpath <- function(dirpath, what="the 'dirpath' slot")
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119: abspath <- file_path_as_absolute(x@dirpath)
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81: filepaths <- file.path(dirpath, filenames)
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13: dirpath="character", # Absolute path to an existing directory.
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48: return(paste0(what, " must be a single string specifying the path ",
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51: return(paste0(what, " must contain the path to an existing directory"))
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122: "path (", abspath, ") to directory ", x@dirpath))
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144: RdsCollection <- function(path=".", filenames=NULL)
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147: msg <- .validate_dirpath(path, what="'path'")
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155: filenames <- dir(path, pattern=pattern, all.files=TRUE)
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158: msg <- .validate_filenames(filenames, path, what="'filenames'")
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176: new2("RdsCollection", dirpath=file_path_as_absolute(path),
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186: setMethod("path", "RdsCollection", function(object) object@dirpath)
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208: readRDS(file.path(path(x), x@filenames[[i]]))
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47: if (!isSingleString(dirpath))
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50: if (!dir.exists(dirpath))
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64: .validate_filenames <- function(filenames, dirpath, what="the 'filenames' slot")
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84: be_what <- paste0("present in directory \"", dirpath, "\"")
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91: function(filepath) {
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92: inherits(try(infoRDS(filepath), silent=TRUE), "try-error")
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115: ## Validate the 'dirpath' slot.
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116: msg <- .validate_dirpath(x@dirpath)
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120: if (abspath != x@dirpath)
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121: return(paste0("the 'dirpath' slot must contain the absolute ",
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125: msg <- .validate_filenames(x@filenames, x@dirpath)
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82: missing_idx <- which(!file.exists(filepaths))
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90: not_ok <- vapply(filepaths,
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XVector:R/RdaCollection-class.R: [ ] |
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45: .get_rdapath <- function(dirpath, objname)
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55: filepath <- .get_rdapath(dirpath, objname)
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99: x_dirpath <- x@dirpath
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110: filepaths <- .get_rdapath(x_dirpath, x_objnames)
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50: file.path(dirpath, filename)
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18: dirpath="character", # a single string
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53: .load_serialized_object <- function(dirpath, objname)
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57: loaded_names <- load(filepath, envir=tempenv)
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59: stop("file '", filepath, "' contains 0 or more ",
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62: stop("serialized object in file '", filepath, "' ",
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77: setGeneric("rdaPath", signature="x",
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78: function(x, objname) standardGeneric("rdaPath")
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82: setMethod("rdaPath", "RdaCollection",
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88: .get_rdapath(x@dirpath, objname)
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137: RdaCollection <- function(dirpath, objnames)
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139: new("RdaCollection", dirpath=dirpath, objnames=objnames)
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161: .load_serialized_object(x@dirpath, i)
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111: missing_idx <- which(!file.exists(filepaths))
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121: filepaths_in_1string <-
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122: paste(paste0("'", filepaths[missing_idx], "'"), collapse=", ")
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124: msg <- c(what, filepaths_in_1string, is_or_are, "missing")
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StarBioTrek:man/path.Rd: [ ] |
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4: \name{path}
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5: \alias{path}
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6: \title{pathway data list}
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9: pathway data list
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gemma.R:man/gemmaPath.Rd: [ ] |
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5: \title{Get gemma path}
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13: Get gemma path
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3: \name{gemmaPath}
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4: \alias{gemmaPath}
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7: gemmaPath()
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MineICA:man/relativePath.Rd: [ ] |
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3: \title{Relative path}
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5: relativePath(path1, path2)
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8: \item{path1}{The first path}
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10: \item{path2}{The second path}
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13: The relative path between path1 and path2
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16: Computes the relative path between two imbricated paths
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19: \code{path1} and \code{path2} must be imbricated.
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22: path1 <- "home/lulu/res/gene2comp/"
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23: path2 <- "home/lulu/res/comp2annot/invasive/"
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24: relativePath(path1,path2)
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1: \name{relativePath}
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2: \alias{relativePath}
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gemma.R:man/setGemmaPath.Rd: [ ] |
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5: \title{Set gemma path}
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7: setGemmaPath(path)
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10: \item{path}{"dev", "prod" or a link to use to access gemma API}
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16: Set gemma path
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3: \name{setGemmaPath}
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4: \alias{setGemmaPath}
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ISAnalytics:man/default_report_path.Rd: [ ] |
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3: \name{default_report_path}
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4: \alias{default_report_path}
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8: default_report_path()
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11: A path
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18: default_report_path()
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rawrr:man/rawrrAssemblyPath.Rd: [ ] |
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5: \title{Derives the path where all .NET assemblies are stored.}
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10: path
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13: Derives the path where all .NET assemblies are stored.
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3: \name{rawrrAssemblyPath}
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4: \alias{rawrrAssemblyPath}
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7: rawrrAssemblyPath()
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16: rawrrAssemblyPath()
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CONFESS:man/pathUpdater.Rd: [ ] |
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7: pathUpdater(data, path)
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10: \item{data}{Data matrix. A matrix of centroids with their path progression indices.}
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12: \item{path}{Numeric vector. The path progression indices.}
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15: The sorted cluster indices (path)
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18: A helper that updates the path sorted clusters after re-estimation by change-point analysis.
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3: \name{pathUpdater}
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4: \alias{pathUpdater}
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5: \title{pathUpdater}
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multiGSEA:man/archivePath.Rd: [ ] |
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5: \title{Retrieve path to a cached file.}
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13: String containing the path to the file.
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16: The function retrieves the path to a file that is cached in the archive
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3: \name{archivePath}
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4: \alias{archivePath}
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7: archivePath(filename)
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CONFESS:man/fixPath.Rd: [ ] |
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18: It tests whether the path has been appropariately defined and produces an error if not.
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3: \name{fixPath}
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4: \alias{fixPath}
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5: \title{FixPath}
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7: fixPath(data, groups)
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TrajectoryGeometry:man/crooked_path_center.Rd: [ ] |
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4: \name{crooked_path_center}
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5: \alias{crooked_path_center}
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6: \title{Crooked path center}
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11: projection of crooked_path.
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18: crooked_path_center
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22: the projection of crooked_path
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rawrr:man/dot-checkDllInMonoPath.Rd: [ ] |
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5: \title{Check if a file is contained in the environment variable \code{MONO_PATH}.}
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16: Check if a file is contained in the environment variable \code{MONO_PATH}.
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3: \name{.checkDllInMonoPath}
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4: \alias{.checkDllInMonoPath}
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7: .checkDllInMonoPath(dll = "ThermoFisher.CommonCore.Data.dll")
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TrajectoryGeometry:man/straight_path.Rd: [ ] |
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4: \name{straight_path}
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5: \alias{straight_path}
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6: \title{Straight path}
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10: The path is roughly in the (1,0,0) direction.
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18: straight_path
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21: A path of n points in dimension d is an n x d matrix. This
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22: particular path is relatively straight.
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CONFESS:man/path.initiator.Rd: [ ] |
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3: \name{path.initiator}
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4: \alias{path.initiator}
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5: \title{path.initiator}
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7: path.initiator(data, where)
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13: the starting point of the progression path.}
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16: A starting point for the progression path
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19: It finds the cluster that initiates the progression path.
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splatter:man/getPathOrder.Rd: [ ] |
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5: \title{Get path order}
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7: getPathOrder(path.from)
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10: \item{path.from}{vector giving the path endpoints that each path originates
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14: Vector giving the order to process paths in.
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17: Identify the correct order to process paths so that preceding paths have
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3: \name{getPathOrder}
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4: \alias{getPathOrder}
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BiocHail:man/osn_1kg_path.Rd: [ ] |
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3: \name{osn_1kg_path}
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4: \alias{osn_1kg_path}
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5: \title{Open Storage Network path to a zip of hail MatrixTable with some 1kg data for the Hail.is GWAS tutorial}
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7: osn_1kg_path()
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13: Open Storage Network path to a zip of hail MatrixTable with some 1kg data for the Hail.is GWAS tutorial
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16: osn_1kg_path()
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StarBioTrek:man/path_KEGG.Rd: [ ] |
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4: \name{path_KEGG}
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5: \alias{path_KEGG}
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6: \title{All pathways data from KEGG}
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7: \format{A list of pathways with the involved genes}
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9: All pathways data from KEGG
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TrajectoryGeometry:man/straight_path_center.Rd: [ ] |
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4: \name{straight_path_center}
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5: \alias{straight_path_center}
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6: \title{Straight path center}
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11: projection of straight_path.
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19: straight_path_center
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23: the projection so straight_path
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ORFik:man/getGtfPathFromTxdb.Rd: [ ] |
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5: \title{Get path of GTF that created txdb}
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16: a character file path, returns NULL if not valid
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3: \name{getGtfPathFromTxdb}
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4: \alias{getGtfPathFromTxdb}
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7: getGtfPathFromTxdb(txdb, stop.error = TRUE)
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BiocHail:man/path_1kg_annotations.Rd: [ ] |
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3: \name{path_1kg_annotations}
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4: \alias{path_1kg_annotations}
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5: \title{generate path to installed annotations file}
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7: path_1kg_annotations()
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10: character(1) path to annotations
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13: generate path to installed annotations file
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19: path_1kg_annotations()
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TrajectoryGeometry:man/straight_path_projection.Rd: [ ] |
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4: \name{straight_path_projection}
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5: \alias{straight_path_projection}
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6: \title{Straight path projection}
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10: The projection of straight_path[2:14,] onto the unit sphere as seen
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11: from straight_path[1,] .
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19: straight_path_projection
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22: The projection of straight_path onto the unit sphere. This is a
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BiocHail:man/osn_ukbb_sumst10k_path.Rd: [ ] |
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3: \name{osn_ukbb_sumst10k_path}
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4: \alias{osn_ukbb_sumst10k_path}
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5: \title{Open Storage Network path to a zip of hail MatrixTable with a small subset of UKBB summary statistics as of 12/25/2022}
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7: osn_ukbb_sumst10k_path()
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10: character(1) path to zip
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13: Open Storage Network path to a zip of hail MatrixTable with a small subset of UKBB summary statistics as of 12/25/2022
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16: osn_ukbb_sumst10k_path()
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ontoProc:man/get_ordo_owl_path.Rd: [ ] |
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2: % Please edit documentation in R/get_ordo_owl_path.R
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3: \name{get_ordo_owl_path}
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4: \alias{get_ordo_owl_path}
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7: get_ordo_owl_path(target = tempdir())
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10: \item{target}{character(1) path to where decompressed owl will live}
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ORFik:man/optimized_txdb_path.Rd: [ ] |
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3: \name{optimized_txdb_path}
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4: \alias{optimized_txdb_path}
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5: \title{Get path for optimization files for txdb}
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7: optimized_txdb_path(txdb, create.dir = FALSE, stop.error = TRUE)
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18: a character file path, returns NULL if not valid
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22: Get path for optimization files for txdb
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TrajectoryGeometry:man/crooked_path_radius.Rd: [ ] |
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4: \name{crooked_path_radius}
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5: \alias{crooked_path_radius}
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6: \title{Crooked path radius}
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11: crooked_path to the point minimizing this mean distance.
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19: crooked_path_radius
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23: crooked_path to the point minimizing this mean distance.
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TrajectoryGeometry:man/crooked_path.Rd: [ ] |
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4: \name{crooked_path}
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5: \alias{crooked_path}
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6: \title{Crooked path}
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10: This path changes direction after the 5th point.
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20: crooked_path
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23: A path of n points in dimension d is an n x d matrix. This
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24: particular path is relatively crooked.
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ORFik:man/findFromPath.Rd: [ ] |
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10: \item{filepaths}{path to all files}
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3: \name{findFromPath}
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4: \alias{findFromPath}
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7: findFromPath(filepaths, candidates, slot = "auto")
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16: else must be a character vector of length 1 or equal length as filepaths.}
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TrajectoryGeometry:man/straight_path_radius.Rd: [ ] |
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4: \name{straight_path_radius}
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5: \alias{straight_path_radius}
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6: \title{Straight path radius}
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11: straight_path to the point minimizing this mean distance.
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19: straight_path_radius
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23: straight_path to the point minimizing this mean distance.
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methylKit:man/getDBPath-methods.Rd: [ ] |
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10: \title{Get path to database of the methylDB objects}
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27: The function returns the path to the flat file database that stores the data
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39: #The path to the database is returned
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4: \name{getDBPath}
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5: \alias{getDBPath}
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6: \alias{getDBPath,methylRawListDB-method}
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7: \alias{getDBPath,methylBaseDB-method}
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8: \alias{getDBPath,methylRawDB-method}
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9: \alias{getDBPath,methylDiffDB-method}
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12: getDBPath(x)
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14: \S4method{getDBPath}{methylRawListDB}(x)
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16: \S4method{getDBPath}{methylBaseDB}(x)
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18: \S4method{getDBPath}{methylRawDB}(x)
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20: \S4method{getDBPath}{methylDiffDB}(x)
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40: getDBPath(methylBaseDB.obj)
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hipathia:man/path_vals.Rd: [ ] |
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4: \name{path_vals}
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5: \alias{path_vals}
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12: data(path_vals)
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24: \code{path_vals <- get_paths_matrix(results)}
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6: \title{Pathways matrix of the BRCA gene expression dataset}
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8: Matrix with 40 columns and 1868 rows. Row names are Pathway IDs
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15: Matrix with 40 columns and 1868 rows. Row names are Pathway IDs
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19: Matrix of pathway activation values for the BRCA dataset. This matrix is
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21: by means of the \code{get_paths_matrix} function.
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20: extracted from the Results object returned by the \code{hipathia} function
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gDRimport:man/result_path-method.Rd: [ ] |
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4: \name{result_path}
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5: \alias{result_path}
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6: \alias{result_path,gdr_test_data-method}
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7: \title{Method result_path}
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9: result_path(x)
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11: \S4method{result_path}{gdr_test_data}(x)
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17: value of slot \code{result_path}
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20: Method for object gdr_test_data - access to slot \code{result_path}
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24: result_file_path <- result_path(td)
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loci2path:man/getPathDescription-methods.Rd: [ ] |
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30: loci=eset.list, path=biocarta)
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31: path.des <- getPathDescription(result, biocarta)
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2: % Please edit documentation in R/allGenerics.R, R/loci2pathResult-methods.R
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6: \alias{getPathDescription,loci2pathResult-method}
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7: \title{Extract description for enriched pathways from query result and
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12: \S4method{getPathDescription}{loci2pathResult}(res, geneset)
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26: This function extracts the pathway description from geneSet object.
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4: \name{getPathDescription}
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5: \alias{getPathDescription}
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10: getPathDescription(res, ...)
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nethet:man/hugepath.Rd: [ ] |
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5: \title{Graphical Lasso path with huge package}
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22: Graphical Lasso path with huge package
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3: \name{hugepath}
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4: \alias{hugepath}
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7: hugepath(s, rholist, penalize.diagonal = NULL, trace = NULL)
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cfDNAPro:man/examplePath.Rd: [ ] |
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5: \title{Get path to cfDNAPro example folder.}
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11: If `NULL`, the path of extdata folder will be returned.}
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14: A string. (i.e. the path.)
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18: directory. This function helps get the path to the data.
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2: % Please edit documentation in R/examplePath.R
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3: \name{examplePath}
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4: \alias{examplePath}
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7: examplePath(data = NULL)
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21: examplePath()
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22: examplePath("groups_picard")
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23: examplePath("step6")
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BgeeCall:man/getWorkingPath.Rd: [ ] |
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8: \title{`working_path` Getter}
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18: the value of the `working_path` slot of the object
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21: Get value of the `working_path` slot
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26: working_path <- getWorkingPath(user)
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4: \name{getWorkingPath}
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5: \alias{getWorkingPath}
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6: \alias{getWorkingPath,UserMetadata-method}
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7: \alias{getWorkingPath,userMetadata}
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10: getWorkingPath(userObject)
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12: \S4method{getWorkingPath}{UserMetadata}(userObject)
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gDRimport:man/manifest_path-method.Rd: [ ] |
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4: \name{manifest_path}
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5: \alias{manifest_path}
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6: \alias{manifest_path,gdr_test_data-method}
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7: \title{Method manifest_path}
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9: manifest_path(x)
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11: \S4method{manifest_path}{gdr_test_data}(x)
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17: value of slot \code{manifest_path}
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20: Method for object gdr_test_data - access to slot \code{manifest_path}
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24: manifest_file_path <- manifest_path(td)
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TrajectoryGeometry:man/crooked_path_projection.Rd: [ ] |
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4: \name{crooked_path_projection}
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5: \alias{crooked_path_projection}
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6: \title{Crooked path projection}
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10: The projection of crooked_path[7:14,] onto the unit sphere as seen
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11: from crooked_path[6,] .
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19: crooked_path_projection
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22: The projection of the last 8 points on crooked_path onto the unit
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StarBioTrek:man/GetPathData.Rd: [ ] |
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7: GetPathData(path_ALL)
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10: \item{path_ALL}{variable. The user can select the variable as obtained by GetData function}
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19: pathway_ALL_GENE<-GetPathData(path_ALL=path[1:3])
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5: \title{Get genes inside pathways.}
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13: a list of pathways
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16: GetPathData creates a list of genes inside the pathways.
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3: \name{GetPathData}
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4: \alias{GetPathData}
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shiny.gosling:man/add_file_to_resource_path.Rd: [ ] |
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3: \name{add_file_to_resource_path}
|
4: \alias{add_file_to_resource_path}
|
7: add_file_to_resource_path(file_path = NULL, object = NULL)
|
10: \item{file_path}{A character. Specify the file_path to the local csv file.}
|
gDRimport:man/template_path-method.Rd: [ ] |
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4: \name{template_path}
|
5: \alias{template_path}
|
6: \alias{template_path,gdr_test_data-method}
|
7: \title{Method template_path}
|
9: template_path(x)
|
11: \S4method{template_path}{gdr_test_data}(x)
|
17: value of slot \code{template_path}
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20: Method for object gdr_test_data - access to slot \code{template_path}
|
24: template_file_path <- template_path(td)
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ramwas:man/isAbsolutePath.Rd: [ ] |
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4: Check if Path is Absolute.
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7: Check whether a path is relative or absolute.
|
10: isAbsolutePath(path)
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13: \item{path}{
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14: Path to be tested.
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21: \code{TRUE} if the path is absolute, \code{FALSE} otherwise.
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29: For instance, "~hi" is not an absolute path.
|
1: \name{isAbsolutePath}
|
2: \alias{isAbsolutePath}
|
18: The function is designed to word with both Windows and Unix paths.
|
32: See also \code{\link{makefullpath}}.
|
35: isAbsolutePath( "C:/123" ) # TRUE
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36: isAbsolutePath( "~123" ) # FALSE
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37: isAbsolutePath( "~/123" ) # TRUE
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38: isAbsolutePath( "/123" ) # TRUE
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39: isAbsolutePath( "\\\\123" ) # TRUE
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40: isAbsolutePath( "asd\\\\123" ) # FALSE
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41: isAbsolutePath( "a\\\\123" ) # FALSE
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StarBioTrek:man/GetPathNet.Rd: [ ] |
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7: GetPathNet(path_ALL)
|
10: \item{path_ALL}{variable. The user can select the variable as obtained by GetData function}
|
19: pathway_net<-GetPathNet(path_ALL=path[1:3])
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5: \title{Get interacting genes inside pathways.}
|
13: a list of pathways
|
16: GetPathNet creates a list of genes inside the pathways.
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3: \name{GetPathNet}
|
4: \alias{GetPathNet}
|
MACSQuantifyR:man/setPath.Rd: [ ] |
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5: \title{sets custom output path}
|
7: setPath(MACSQuant,path=NULL)
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14: \item{path}{user defined path, default is tempd}
|
17: object of class MACSQuant with updated path
|
20: This function allows the user to set the output directory path
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26: user_path="."
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27: #MACSQuant = setPath(MACSQuant,path=user_path)
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3: \name{setPath}
|
4: \alias{setPath}
|
23: filepath <- system.file("extdata", "SingleDrugs.xlsx",
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25: #MACSQuant = load_MACSQuant(filepath)
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ggtree:man/get.path.Rd: [ ] |
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3: \name{get.path}
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4: \alias{get.path}
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5: \title{get.path}
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7: get.path(phylo, from, to)
|
20: path from start node to end node
|
xcms:man/phenoDataFromPaths.Rd: [ ] |
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11: path) of the experiment's files.}
|
5: \title{Derive experimental design from file paths}
|
7: phenoDataFromPaths(paths)
|
10: \item{paths}{\code{character} representing the file names (including the full
|
3: \name{phenoDataFromPaths}
|
4: \alias{phenoDataFromPaths}
|
14: The \code{phenoDataFromPaths} function builds a \code{data.frame}
|
ramwas:man/makefullpath.Rd: [ ] |
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4: Combine Path and Filename into Filename with Path
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7: Combine a path with a filename into filename with path.
|
10: makefullpath(path, filename)
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13: \item{path}{
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14: Path, relative to which the filename is expected to be.
|
18: Can be just filename, include relative path, or
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19: include absolute path.
|
23: Function returns \code{filename} if it includes absolute path or
|
24: if \code{path} is \code{NULL}.
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27: Filename with the path included.
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42: # Path is ignored if the filename already includes absolute path
|
1: \name{makefullpath}
|
2: \alias{makefullpath}
|
33: See also \code{\link{isAbsolutePath}}.
|
36: makefullpath("dir1/dir2", "file.txt")
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39: makefullpath("dir1/dir2", "dir3/file.txt")
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44: makefullpath("dir1/dir2", "/file.txt")
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47: makefullpath("dir1/dir2", "C:/file.txt")
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hipathia:man/get_pathway_functions.Rd: [ ] |
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27: \item{unique}{Boolean, whether to return the first function for each path.}
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3: \name{get_pathway_functions}
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4: \alias{get_pathway_functions}
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5: \title{Returns functions related to a pathway}
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7: get_pathway_functions(
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8: pathigraph,
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16: \item{pathigraph}{Pathway object}
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24: nodes of the pathways or not. If FALSE, functions will refer to all the nodes
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25: of the pathway.}
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30: List of annotations from pathways to functions
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33: Returns functions related to a pathway
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gespeR:man/path-methods.Rd: [ ] |
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4: \name{path<-}
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5: \alias{path<-}
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6: \alias{path<-,TargetRelations,character-method}
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7: \title{path}
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9: path(object) <- value
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11: \S4method{path}{TargetRelations,character}(object) <- value
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16: \item{value}{A string defining the path}
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19: A \code{\linkS4class{TargetRelations}} object with set path
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22: Set the path of a a \code{\linkS4class{TargetRelations}} object object
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26: path(trels) <- "/dev/null"
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sitadela:man/getsetDbPath.Rd: [ ] |
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4: \title{Get and set sitadela default database path}
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10: \item{db}{path to a valid SQLite database file.}
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17: used to set and get the path to a sitadela annotation
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19: \code{file.path(system.file(package="sitadela"),"annotation.sqlite")}.
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21: environment pointing to the desired path.
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1: \name{getsetDbPath}
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2: \alias{setDbPath}
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3: \alias{getDbPath}
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6: setDbPath(db = NULL)
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7: getDbPath()
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16: The \code{setDbPath} and \code{getDbPath} functions are
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24: myPath <- "/home/me/test.sqlite"
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25: setDbPath(myPath)
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26: getDbPath()
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