Found 29352 results in 8035 files, showing top 50 files (show more).
XVector:R/RdsCollection-class.R: [ ]
45: .validate_dirpath <- function(dirpath, what="the 'dirpath' slot")
119:     abspath <- file_path_as_absolute(x@dirpath)
81:     filepaths <- file.path(dirpath, filenames)
13:         dirpath="character",   # Absolute path to an existing directory.
48:         return(paste0(what, " must be a single string specifying the path ",
51:         return(paste0(what, " must contain the path to an existing directory"))
122:                       "path (", abspath, ") to directory ", x@dirpath))
144: RdsCollection <- function(path=".", filenames=NULL)
147:     msg <- .validate_dirpath(path, what="'path'")
155:         filenames <- dir(path, pattern=pattern, all.files=TRUE)
158:         msg <- .validate_filenames(filenames, path, what="'filenames'")
176:     new2("RdsCollection", dirpath=file_path_as_absolute(path),
186: setMethod("path", "RdsCollection", function(object) object@dirpath)
208:         readRDS(file.path(path(x), x@filenames[[i]]))
47:     if (!isSingleString(dirpath))
50:     if (!dir.exists(dirpath))
64: .validate_filenames <- function(filenames, dirpath, what="the 'filenames' slot")
84:         be_what <- paste0("present in directory \"", dirpath, "\"")
91:         function(filepath) {
92:             inherits(try(infoRDS(filepath), silent=TRUE), "try-error")
115:     ## Validate the 'dirpath' slot.
116:     msg <- .validate_dirpath(x@dirpath)
120:     if (abspath != x@dirpath)
121:         return(paste0("the 'dirpath' slot must contain the absolute ",
125:     msg <- .validate_filenames(x@filenames, x@dirpath)
82:     missing_idx <- which(!file.exists(filepaths))
90:     not_ok <- vapply(filepaths,
XVector:R/RdaCollection-class.R: [ ]
45: .get_rdapath <- function(dirpath, objname)
55:     filepath <- .get_rdapath(dirpath, objname)
99:     x_dirpath <- x@dirpath
110:     filepaths <- .get_rdapath(x_dirpath, x_objnames)
50:     file.path(dirpath, filename)
18:         dirpath="character",   # a single string
53: .load_serialized_object <- function(dirpath, objname)
57:     loaded_names <- load(filepath, envir=tempenv)
59:         stop("file '", filepath, "' contains 0 or more ",
62:         stop("serialized object in file '", filepath, "' ",
77: setGeneric("rdaPath", signature="x",
78:     function(x, objname) standardGeneric("rdaPath")
82: setMethod("rdaPath", "RdaCollection",
88:         .get_rdapath(x@dirpath, objname)
137: RdaCollection <- function(dirpath, objnames)
139:     new("RdaCollection", dirpath=dirpath, objnames=objnames)
161:         .load_serialized_object(x@dirpath, i)
111:     missing_idx <- which(!file.exists(filepaths))
121:         filepaths_in_1string <-
122:             paste(paste0("'", filepaths[missing_idx], "'"), collapse=", ")
124:         msg <- c(what, filepaths_in_1string, is_or_are, "missing")
StarBioTrek:man/path.Rd: [ ]
4: \name{path}
5: \alias{path}
6: \title{pathway data list}
9: pathway data list
MineICA:man/relativePath.Rd: [ ]
3: \title{Relative path}
5:   relativePath(path1, path2)
8:   \item{path1}{The first path}
10:   \item{path2}{The second path}
13:   The relative path between path1 and path2
16:   Computes the relative path between two imbricated paths
19:   \code{path1} and \code{path2} must be imbricated.
22: path1 <- "home/lulu/res/gene2comp/"
23: path2 <- "home/lulu/res/comp2annot/invasive/"
24: relativePath(path1,path2)
1: \name{relativePath}
2: \alias{relativePath}
ISAnalytics:man/default_report_path.Rd: [ ]
3: \name{default_report_path}
4: \alias{default_report_path}
8: default_report_path()
11: A path
18: default_report_path()
CONFESS:man/pathUpdater.Rd: [ ]
7: pathUpdater(data, path)
10: \item{data}{Data matrix. A matrix of centroids with their path progression indices.}
12: \item{path}{Numeric vector. The path progression indices.}
15: The sorted cluster indices (path)
18: A helper that updates the path sorted clusters after re-estimation by change-point analysis.
3: \name{pathUpdater}
4: \alias{pathUpdater}
5: \title{pathUpdater}
multiGSEA:man/archivePath.Rd: [ ]
5: \title{Retrieve path to a cached file.}
13: String containing the path to the file.
16: The function retrieves the path to a file that is cached in the archive
3: \name{archivePath}
4: \alias{archivePath}
7: archivePath(filename)
CONFESS:man/fixPath.Rd: [ ]
18: It tests whether the path has been appropariately defined and produces an error if not.
3: \name{fixPath}
4: \alias{fixPath}
5: \title{FixPath}
7: fixPath(data, groups)
TrajectoryGeometry:man/crooked_path_center.Rd: [ ]
4: \name{crooked_path_center}
5: \alias{crooked_path_center}
6: \title{Crooked path center}
11:     projection of crooked_path.
18: crooked_path_center
22:     the projection of crooked_path
ORFik:man/getGtfPathFromTxdb.Rd: [ ]
5: \title{Get path of GTF that created txdb}
16: a character file path, returns NULL if not valid
3: \name{getGtfPathFromTxdb}
4: \alias{getGtfPathFromTxdb}
7: getGtfPathFromTxdb(txdb, stop.error = TRUE)
TrajectoryGeometry:man/straight_path.Rd: [ ]
4: \name{straight_path}
5: \alias{straight_path}
6: \title{Straight path}
10: The path is roughly in the (1,0,0) direction.
18: straight_path
21: A path of n points in dimension d is an n x d matrix.  This
22: particular path is relatively straight.
CONFESS:man/path.initiator.Rd: [ ]
3: \name{path.initiator}
4: \alias{path.initiator}
5: \title{path.initiator}
7: path.initiator(data, where)
13: the starting point of the progression path.}
16: A starting point for the progression path
19: It finds the cluster that initiates the progression path.
rawrr:man/rawrrAssemblyPath.Rd: [ ]
5: \title{Derives the path where all .NET assemblies are stored.}
10: path
13: Derives the path where all .NET assemblies are stored.
3: \name{rawrrAssemblyPath}
4: \alias{rawrrAssemblyPath}
7: rawrrAssemblyPath()
16: rawrrAssemblyPath()
splatter:man/getPathOrder.Rd: [ ]
5: \title{Get path order}
7: getPathOrder(path.from)
10: \item{path.from}{vector giving the path endpoints that each path originates
14: Vector giving the order to process paths in.
17: Identify the correct order to process paths so that preceding paths have
3: \name{getPathOrder}
4: \alias{getPathOrder}
StarBioTrek:man/path_KEGG.Rd: [ ]
4: \name{path_KEGG}
5: \alias{path_KEGG}
6: \title{All pathways data from KEGG}
7: \format{A list of pathways with the involved genes}
9: All pathways data from KEGG
ORFik:man/optimized_txdb_path.Rd: [ ]
3: \name{optimized_txdb_path}
4: \alias{optimized_txdb_path}
5: \title{Get path for optimization files for txdb}
7: optimized_txdb_path(txdb, create.dir = FALSE, stop.error = TRUE)
18: a character file path, returns NULL if not valid
22: Get path for optimization files for txdb
TrajectoryGeometry:man/straight_path_center.Rd: [ ]
4: \name{straight_path_center}
5: \alias{straight_path_center}
6: \title{Straight path center}
11:     projection of straight_path.
19: straight_path_center
23:     the projection so straight_path
TrajectoryGeometry:man/straight_path_projection.Rd: [ ]
4: \name{straight_path_projection}
5: \alias{straight_path_projection}
6: \title{Straight path projection}
10: The projection of straight_path[2:14,] onto the unit sphere as seen
11:     from straight_path[1,] .
19: straight_path_projection
22: The projection of straight_path onto the unit sphere.  This is a
ORFik:man/findFromPath.Rd: [ ]
10: \item{filepaths}{path to all files}
3: \name{findFromPath}
4: \alias{findFromPath}
7: findFromPath(filepaths, candidates, slot = "auto")
16: else must be a character vector of length 1 or equal length as filepaths.}
cfDNAPro:man/examplePath.Rd: [ ]
5: \title{Get path to cfDNAPro example folder.}
11: If `NULL`, the path of extdata folder will be returned.}
14: A string. (i.e. the path.)
18: directory. This function helps get the path to the data.
2: % Please edit documentation in R/examplePath.R
3: \name{examplePath}
4: \alias{examplePath}
7: examplePath(data = NULL)
21: examplePath()
22: examplePath("groups_picard")
23: examplePath("step6")
TrajectoryGeometry:man/crooked_path_radius.Rd: [ ]
4: \name{crooked_path_radius}
5: \alias{crooked_path_radius}
6: \title{Crooked path radius}
11: crooked_path to the point minimizing this mean distance.
19: crooked_path_radius
23: crooked_path to the point minimizing this mean distance.
TrajectoryGeometry:man/crooked_path.Rd: [ ]
4: \name{crooked_path}
5: \alias{crooked_path}
6: \title{Crooked path}
10: This path changes direction after the 5th point.
20: crooked_path
23: A path of n points in dimension d is an n x d matrix.  This
24: particular path is relatively crooked.
TrajectoryGeometry:man/straight_path_radius.Rd: [ ]
4: \name{straight_path_radius}
5: \alias{straight_path_radius}
6: \title{Straight path radius}
11: straight_path to the point minimizing this mean distance.
19: straight_path_radius
23: straight_path to the point minimizing this mean distance.
hipathia:man/path_vals.Rd: [ ]
4: \name{path_vals}
5: \alias{path_vals}
10: data(path_vals)
22: \code{path_vals <- get_paths_matrix(results)}
6: \title{Pathways matrix of the BRCA gene expression dataset}
7: \format{Matrix with 40 columns and 1868 rows. Row names are Pathway IDs
13: Matrix with 40 columns and 1868 rows. Row names are Pathway IDs
17: Matrix of pathway activation values for the BRCA dataset. This matrix is
19: by means of the \code{get_paths_matrix} function.
18: extracted from the Results object returned by the \code{hipathia} function
methylKit:man/getDBPath-methods.Rd: [ ]
10: \title{Get path to database of the methylDB objects}
27: The function returns the path to the flat file database that stores the data 
39: #The path to the database is returned
4: \name{getDBPath}
5: \alias{getDBPath}
6: \alias{getDBPath,methylRawListDB-method}
7: \alias{getDBPath,methylBaseDB-method}
8: \alias{getDBPath,methylRawDB-method}
9: \alias{getDBPath,methylDiffDB-method}
12: getDBPath(x)
14: \S4method{getDBPath}{methylRawListDB}(x)
16: \S4method{getDBPath}{methylBaseDB}(x)
18: \S4method{getDBPath}{methylRawDB}(x)
20: \S4method{getDBPath}{methylDiffDB}(x)
40: getDBPath(methylBaseDB.obj)
loci2path:man/getPathDescription-methods.Rd: [ ]
30:   loci=eset.list, path=biocarta)
31: path.des <- getPathDescription(result, biocarta)
2: % Please edit documentation in R/allGenerics.R, R/loci2pathResult-methods.R
6: \alias{getPathDescription,loci2pathResult-method}
7: \title{Extract description for enriched pathways from query result and 
12: \S4method{getPathDescription}{loci2pathResult}(res, geneset)
26: This function extracts the pathway description from geneSet object.
4: \name{getPathDescription}
5: \alias{getPathDescription}
10: getPathDescription(res, ...)
nethet:man/hugepath.Rd: [ ]
5: \title{Graphical Lasso path with huge package}
22: Graphical Lasso path with huge package
3: \name{hugepath}
4: \alias{hugepath}
7: hugepath(s, rholist, penalize.diagonal = NULL, trace = NULL)
TrajectoryGeometry:man/crooked_path_projection.Rd: [ ]
4: \name{crooked_path_projection}
5: \alias{crooked_path_projection}
6: \title{Crooked path projection}
10: The projection of crooked_path[7:14,] onto the unit sphere as seen
11:     from crooked_path[6,] .
19: crooked_path_projection
22: The projection of the last 8 points on crooked_path onto the unit
StarBioTrek:man/GetPathData.Rd: [ ]
7: GetPathData(path_ALL)
10: \item{path_ALL}{variable. The user can select the variable as obtained by  GetData function}
19: pathway_ALL_GENE<-GetPathData(path_ALL=path[1:3])
5: \title{Get  genes inside pathways.}
13: a list of pathways
16: GetPathData creates a list of genes inside the pathways.
3: \name{GetPathData}
4: \alias{GetPathData}
BgeeCall:man/getWorkingPath.Rd: [ ]
8: \title{`working_path` Getter}
18: the value of the `working_path` slot of the object
21: Get value of the `working_path` slot
26: working_path <- getWorkingPath(user)
4: \name{getWorkingPath}
5: \alias{getWorkingPath}
6: \alias{getWorkingPath,UserMetadata-method}
7: \alias{getWorkingPath,userMetadata}
10: getWorkingPath(userObject)
12: \S4method{getWorkingPath}{UserMetadata}(userObject)
ramwas:man/isAbsolutePath.Rd: [ ]
4:     Check if Path is Absolute.
7:     Check whether a path is relative or absolute.
10: isAbsolutePath(path)
13:     \item{path}{
14:         Path to be tested.
21:     \code{TRUE} if the path is absolute, \code{FALSE} otherwise.
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
36: isAbsolutePath( "~123" )     # FALSE
37: isAbsolutePath( "~/123" )    # TRUE
38: isAbsolutePath( "/123" )     # TRUE
39: isAbsolutePath( "\\\\123" )    # TRUE
40: isAbsolutePath( "asd\\\\123" ) # FALSE
41: isAbsolutePath( "a\\\\123" )   # FALSE
StarBioTrek:man/GetPathNet.Rd: [ ]
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])
5: \title{Get  interacting genes inside pathways.}
13: a list of pathways
16: GetPathNet creates a list of genes inside the pathways.
3: \name{GetPathNet}
4: \alias{GetPathNet}
MACSQuantifyR:man/setPath.Rd: [ ]
5: \title{sets custom output path}
7: setPath(MACSQuant,path=NULL)
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
26: user_path="."
27: #MACSQuant = setPath(MACSQuant,path=user_path)
3: \name{setPath}
4: \alias{setPath}
23: filepath <- system.file("extdata", "SingleDrugs.xlsx",
25: #MACSQuant = load_MACSQuant(filepath)
xcms:man/phenoDataFromPaths.Rd: [ ]
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: [ ]
4:     Combine Path and Filename into  Filename with Path
7:     Combine a path with a filename into filename with path.
10: makefullpath(path, filename)
13:     \item{path}{
14:         Path, relative to which the filename is expected to be.
18:         Can be just filename, include relative path, or
19:         include absolute path.
23:     Function returns \code{filename} if it includes absolute path or
24:     if \code{path} is \code{NULL}.
27:     Filename with the path included.
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")
39: makefullpath("dir1/dir2", "dir3/file.txt")
44: makefullpath("dir1/dir2", "/file.txt")
47: makefullpath("dir1/dir2", "C:/file.txt")
hipathia:man/get_pathway_functions.Rd: [ ]
22: \item{unique}{Boolean, whether to return the first function for each path.}
3: \name{get_pathway_functions}
4: \alias{get_pathway_functions}
5: \title{Returns functions related to a pathway}
7: get_pathway_functions(pathigraph, dbannot, entrez2hgnc,
11: \item{pathigraph}{Pathway object}
19: nodes of the pathways or not. If FALSE, functions will refer to all the nodes
20: of the pathway.}
25: List of annotations from pathways to functions
28: Returns functions related to a pathway
gespeR:man/path-methods.Rd: [ ]
4: \name{path<-}
5: \alias{path<-}
6: \alias{path<-,TargetRelations,character-method}
7: \title{path}
9: path(object) <- value
11: \S4method{path}{TargetRelations,character}(object) <- value
16: \item{value}{A string defining the path}
19: A \code{\linkS4class{TargetRelations}} object with set path
22: Set the path of a a \code{\linkS4class{TargetRelations}} object object
26: path(trels) <- "/dev/null"
peakPantheR:man/spectraPaths_and_metadata_UI_helper.Rd: [ ]
16: \item{spectraMetadataPath}{NULL or path to a csv of spectra metadata, with
31: input_spectraPaths    <- c('./path/file1', './path/file2', './path/file3')
5: \title{UI data import helper - prepare file paths and metadata}
9:     spectraMetadataPath = NULL
13: \item{spectraPaths}{NULL or character vector of spectra file paths, to set
17: spectra as row and metadata as columns. (spectraPaths in column `filepath`)}
26: the `filepath` column
30: # spectraPath
36:                             dimnames=list(c(),c('filepath', 'testcol')),
40: spectraMetaPath <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.csv')
43:                     file=spectraMetaPath,
48:                                     spectraMetadataPath = spectraMetaPath)
3: \name{spectraPaths_and_metadata_UI_helper}
4: \alias{spectraPaths_and_metadata_UI_helper}
7: spectraPaths_and_metadata_UI_helper(
8:     spectraPaths = NULL,
20: spectraPaths (str) and spectraMetadata (DataFrame or NULL) read from
24: Return spectraPaths and spectraMetadata from a .csv file (if available).
25: If reading from the spectraMetadata file, the spectraPaths are taken from
34: input_spectraMetadata <- data.frame(matrix(data=c(input_spectraPaths,
47: spectraPaths_and_metadata_UI_helper(spectraPaths = NULL,
sitadela:man/getsetDbPath.Rd: [ ]
4: \title{Get and set sitadela default database path}
10:     \item{db}{path to a valid SQLite database file.}
17:     used to set and get the path to a sitadela annotation
19:     \code{file.path(system.file(package="sitadela"),"annotation.sqlite")}.
21:     environment pointing to the desired path.
1: \name{getsetDbPath}
2: \alias{setDbPath}
3: \alias{getDbPath}
6:     setDbPath(db = NULL)
7:     getDbPath()
16:     The \code{setDbPath} and \code{getDbPath} functions are 
24: myPath <- "/home/me/test.sqlite"
25: setDbPath(myPath)
26: getDbPath()
CONFESS:man/estimatePath.Rd: [ ]
13: It can be either "clockwise" or "anticlockwise" depending on how the path is expected
16: \item{start}{Integer. The cluster number that is assigned as the path starting point}
19: The sorted cluster indices (path)
22: The main function for automatic path estimation .
3: \name{estimatePath}
4: \alias{estimatePath}
5: \title{estimatePath}
7: estimatePath(data, type, start)
NetPathMiner:man/NetPathMiner-package.Rd: [ ]
8: \title{General framework for network extraction, path mining.}
10: NetPathMiner implements a flexible module-based process flow for network path mining and visualization,
13: formats, enabling its utility to most common pathway databases.
15: thousands of output paths.
4: \name{NetPathMiner-package}
5: \alias{NetPathMiner-package}
6: \alias{NetPathMiner}
12: NetPathMiner supports construction of various types of genome scale networks from KGML, SBML and BioPAX
14: NetPathMiner also provides different visualization techniques to facilitate the analysis of even
netDx:man/getGMjar_path.Rd: [ ]
3: \name{getGMjar_path}
4: \alias{getGMjar_path}
7: getGMjar_path(verbose = FALSE)
13: (char) Path to local cached copy of GeneMANIA jar file..
20: getGMjar_path()
ggtree:man/get.path.Rd: [ ]
3: \name{get.path}
4: \alias{get.path}
5: \title{get.path}
7: get.path(phylo, from, to)
20: path from start node to end node
Category:man/probes2Path.Rd: [ ]
1: \name{probes2Path}
2: \alias{probes2Path}
9: probes2Path(pids, data = "hgu133plus2")
17:   This is a simple look up in the appropriate chip \code{PATH} data
30:  probes2Path(x, "hgu95av2.db")
3: \title{A function to map probe identifiers to pathways. }
6:  up all KEGG pathways that the probe is documented to be involved in.
21:  A list of pathway vectors. One element for each value of \code{pid}
22:  that is mapped to at least one pathway.
ggmanh:man/default_gds_path.Rd: [ ]
3: \name{default_gds_path}
4: \alias{default_gds_path}
5: \title{Path to Default GDS File}
7: default_gds_path()
13: Find path to the default gds file.
16: default_gds_path()
fgsea:man/gmtPathways.Rd: [ ]
10: \item{gmt.file}{Path to a GMT file.}
2: % Please edit documentation in R/pathways.R
5: \title{Returns a list of pathways from a GMT file.}
16: Returns a list of pathways from a GMT file.
19: pathways <- gmtPathways(system.file(
3: \name{gmtPathways}
4: \alias{gmtPathways}
7: gmtPathways(gmt.file)
hipathia:man/normalize_paths.Rd: [ ]
7: normalize_paths(path_vals, metaginfo)
10: \item{path_vals}{SummarizedExperiment or matrix of the pathway values}
16: depending on the class of \code{path_vals}.
30: data(path_vals)
33: path_normalized <- normalize_paths(path_vals, pathways)
3: \name{normalize_paths}
4: \alias{normalize_paths}
5: \title{Normalize the pathway matrix by rows}
12: \item{metaginfo}{Pathways object}
15: SummarizedExperiment or matrix of normalized pathway values, 
19: Due to the nature of the Hipathia method, the length of a pathway may
31: pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
21: subpathways, we strongly recommend to normalize the matrix with this
25: This function removes the bias caused by the length of the subpathways
VanillaICE:man/parsedPath.Rd: [ ]
6: \title{Complete path to directory for keeping parsed files}
16: A character string indicating the complete path for storing parsed
3: \name{parsedPath}
4: \alias{parsedPath}
5: \alias{parsedPath,ArrayViews-method}
8: parsedPath(object)
10: \S4method{parsedPath}{ArrayViews}(object)
DIAlignR:man/plotAlignmentPath.Rd: [ ]
5: \title{Visualize alignment path through similarity matrix}
16: Plot aligned path through the similarity matrix. Reference run has indices on X-axis, eXp run has them on Y-axis.
3: \name{plotAlignmentPath}
4: \alias{plotAlignmentPath}
7: plotAlignmentPath(AlignObjOutput)
21: dataPath <- system.file("extdata", package = "DIAlignR")
24: AlignObjOutput <- getAlignObjs(analytes = 4618L, runs, dataPath = dataPath, objType = "medium")
25: plotAlignmentPath(AlignObjOutput)
systemPipeR:man/tryPath.Rd: [ ]
7: Function to check if the full path (file or directory) exists. 
10: tryPath(path)
13:   \item{path}{
14: a character vector of full path name.
18: This function produces a character vector of the file or directory name defined on the \code{path} argument.
21: A character vector containing the name of the file or directory. If the path does not exist, it will return an error message. 
28: tryPath(path=file)
1: \name{tryPath}
2: \alias{tryPath}