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R.filesets (version 2.15.0)

Easy Handling of and Access to Files Organized in Structured Directories

Description

A file set refers to a set of files located in one or more directories on the file system. This package provides classes and methods to locate, setup, subset, navigate and iterate such sets. The API is designed such that these classes can be extended via inheritance to provide a richer API for special file formats. Moreover, a specific name format is defined such that filenames and directories can be considered to have full names which consists of a name followed by comma-separated tags. This adds additional flexibility to identify file sets and individual files. NOTE: This package's API should be considered to be in an beta stage. Its main purpose is currently to support the aroma.* packages, where it is one of the main core components; if you decide to build on top of this package, please contact the author first.

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Install

install.packages('R.filesets')

Monthly Downloads

567

Version

2.15.0

License

LGPL (>= 2.1)

Issues

Pull Requests

Stars

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Repository

https://github.com/HenrikBengtsson/R.filesets

Homepage

https://www.aroma-project.org/

Maintainer

Henrik Bengtsson

Last Published

July 21st, 2022

Functions in R.filesets (2.15.0)

GenericDataFileSet

The GenericDataFileSet class

ChecksumFileSet

The ChecksumFileSet class

The ChecksumFile class

ColumnNamesInterface

The ColumnNamesInterface class interface

GenericDataFile

The abstract GenericDataFile class

FullNameInterface

The FullNameInterface class interface

GenericTabularFile

The abstract GenericTabularFile class

GenericTabularFileSet

The GenericTabularFileSet class

GenericDataFileSetList

The GenericDataFileSetList class

Deprecated and defunct objects

Deprecated and defunct objects

TabularTextFile

The TabularTextFile class

TabularTextFileSet

The TabularTextFileSet class

append.GenericDataFileSet

Appends one data set to an existing one

anyNA.GenericDataFileSet

Checks whether any of the pathnames are missing

The RdsFile class

R.filesets-package

Package R.filesets

Non-documented objects

Non-documented objects

GenericDataFileSet$byPath

Defines a GenericDataFileSet by searching for files in a directory

GenericDataFileSet$byName

Locates and sets up a file set by its name

The RDataFile class

The RdsFileSet class

compareChecksum.GenericDataFile

Compares the file checksum with the value of the checksum file

extractMatrix.GenericTabularFile

Reads one of the columns

getDefaultFullName.GenericDataFile

Gets the full name of the file

extract.GenericDataFileSet

Extract a subset of the file set

getDefaultFullName.GenericDataFileSet

Gets the default full name of the file set

The RDataFileSet class

getChecksumObjects.GenericDataFileSet

Retrieves objects that uniquely identifying the data set

getColumnNames.ColumnNamesInterface

Gets the column names

copyTo.GenericDataFile

Safely copies a file to a new pathname

getFilename.GenericDataFile

Gets the filename of the file

getFullName.FullNameInterface

Gets the full name

GenericDataFileSet$findByName

Locates all file sets that match the requested name

GenericDataFile$fromFile

Defines a GenericDataFile from a pathname

dim.GenericTabularFile

Gets the dimension of data table

copyTo.GenericDataFileSet

Copies a data set to another directory

hasTags.FullNameInterface

Checks whether the fullname contains a given set of tag(s)

hasColumnHeader.TabularTextFile

Checks if there are column names in the header

getDefaultColumnNames.TabularTextFile

Gets the default column names

getChecksum.GenericDataFileSet

Generates a deterministic checksum for an R object

getDefaultFullName.FullNameInterface

Gets the default full name

getFileSize.GenericDataFile

Gets the size of a file

getChecksum.GenericDataFile

Gets the checksum of a file

as.character.GenericDataFile

Returns a short string describing the file

appendFiles.GenericDataFileSet

Appends a list of files to a data set

getFileType.GenericDataFile

Gets the file type of a file

getHeader.TabularTextFile

Gets the file header

getLastAccessedOn.GenericDataFile

Gets when the file was last accessed

as.character.GenericDataFileSet

Returns a short string describing the file set

readDataFrame.TabularTextFile

Reads the tabular data as a data frame

validateChecksum.GenericDataFile

Asserts that the file checksum matches the one of the checksum file

validate.GenericDataFileSet

Validates all files in the data set

as.list.GenericDataFileSet

Returns the files of the file set

getPath.GenericDataFile

Gets the path (directory) of the file

getNames.GenericDataFileSet

Gets the names (or fullnames) of the files in the file set

readChecksum.GenericDataFile

Reads the value of the corresponding checksum file

setColumnNames.ColumnNamesInterface

Sets the column names

getDefaultColumnNames.ColumnNamesInterface

Gets the default column names

isFile.GenericDataFile

Checks if this is an existing file

indexOf.GenericDataFileSet

Finds indices of a subset of files

getPathnames.GenericDataFileSet

Gets the pathnames of the files in the file set

getName.FullNameInterface

getLastModifiedOn.GenericDataFile

Gets when the file was last modified

Arguments$getTags

Gets and validates tags

Reads data from a RDS file

Reads data from a RDS file

readLines.TabularTextFile

Reads the lines of the data file as strings

readDataFrame.TabularTextFileSet

Reads the tabular data from all files as data frames

length.GenericDataFileSet

Gets the number of files in the set

linkTo.GenericDataFile

Creates a symbolic file link

setName.FullNameInterface

Sets the name part of the fullname

sortBy.GenericDataFileSet

setTags.FullNameInterface

nbrOfRows.TabularTextFile

Counts the number of data rows

getFile.GenericDataFileSet

Get a particular file of the file set

getTags.FullNameInterface

readDataFrame.GenericTabularFile

Reads the tabular data as a data frame

nbrOfColumns.ColumnNamesInterface

Gets the number of columns

readColumns.GenericTabularFile

Reads a subset of the columns as a data frame

gzip.GenericDataFile

Compresses/uncompresses a file

dsApplyInPairs.GenericDataFileSet

Applies a function to each pair of file in two file sets

getCreatedOn.GenericDataFile

Gets when the file was created

equals.GenericDataFile

Checks if a file equals another

getExtension.GenericDataFile

Gets the filename extension

gzip.GenericDataFileSet

Compresses/uncompresses a set of files

hasBeenModified.GenericDataFile

Checks whether the file has been modified

getPath.GenericDataFileSet

Gets the path (directory) of the file set

readChecksum.ChecksumFile

Reads the checksum value

getPathname.GenericDataFile

Gets the pathname of the file

nbrOfRows.GenericTabularFile

Gets the number of data rows

setFullName.FullNameInterface

Sets the full name

Reads data from a tabular file

writeColumnsToFiles.GenericTabularFile

Read each column from a data file and exports it to a separate file

validate.ChecksumFile

Asserts that the checksum matches the checksum of file

validate.GenericDataFile

Validates the content of a file

nbrOfLines.TabularTextFile

Counts the number of lines in the data file

renameTo.GenericDataFile

Renames/moves a file

writeChecksum.GenericDataFile

Write the file checksum to a checksum file