| Title: | Converting experimental metadata from ISA-tab into Bioconductor data structures |
|---|---|
| Description: | The Investigation / Study / Assay (ISA) tab-delimited format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from experiments employing a combination of technologies, spanning from traditional approaches to high-throughput techniques. Risa allows to access metadata/data in ISA-Tab format and build Bioconductor data structures. Currently, data generated from microarray, flow cytometry and metabolomics-based (i.e. mass spectrometry) assays are supported. The package is extendable and efforts are undergoing to support metadata associated to proteomics assays. |
| Authors: | Alejandra Gonzalez-Beltran, Audrey Kauffmann, Steffen Neumann, Gabriella Rustici, ISA Team |
| Maintainer: | Alejandra Gonzalez-Beltran <[email protected]> |
| License: | LGPL |
| Version: | 1.47.0 |
| Built: | 2024-07-02 03:34:25 UTC |
| Source: | https://github.com/bioc/Risa |
"AssayTab", a class for maintaing the information of AssayTabThis class maintains information from an AssayTab dataset, including an investigation file, one or more study files, and one or more assay files for each study file.
Objects can be created by calls of the form new("AssayTab", ...).
pathObject of class "character", it represents the path of the ISA-Tab dataset to which this AssayTab belongs
study.filenameObject of class "character" with the filename of the study to which this assay belongs to.
study.identifierObject of class "character" with the identifier of the study to which this assay belongs to.
assay.filenameObject of class "character" with the filename of the assay.
assay.fileObject of class "data.frame" with the contents of the assay file.
assay.technology.typeObject of class "character" with the technology type of this assay.
assay.measurement.typeObject of class "character" with the measurement type of this assay.
assay.namesObject of class "data.frame" with the assay names for this assay file.
data.filenamesObject of class "data.frame" with the data filenames.
signature(x = "AssayTab"): ...
signature(.Object = "AssayTab", full.path="logical"): returns the raw data filenames for this assay
Alejandra Gonzalez-Beltran, [email protected]
ISATab-class,ISATab-methods,
showClass("AssayTab") showClass("MSAssayTab") showClass("MicroarrayAssayTab") showClass("SeqAssayTab") showClass("NMRAssayTab")showClass("AssayTab") showClass("MSAssayTab") showClass("MicroarrayAssayTab") showClass("SeqAssayTab") showClass("NMRAssayTab")
Retrieves an AnnotatedDataFrameAssay.
getAnnotatedDataFrameAssay(isa, assay.filename)getAnnotatedDataFrameAssay(isa, assay.filename)
isa |
An object of the |
assay.filename |
An annotated data frame.
Alejandra Gonzalez-Beltran
ISATab-class, AnnotatedDataFrame
faahkoISAzip <- system.file("extdata","faahKO-metadata.zip", package="Risa") faahkoISA <- readISAtab(zipfile = faahkoISAzip, path = file.path(system.file("extdata", package="Risa"),"faahkoISA"), verbose =TRUE) faahkoADF <- getAnnotatedDataFrameAssay(faahkoISA, [email protected][[1]]) str(faahkoADF) armstrongISAzip <- system.file("extdata","ARMSTRONG-S-3-metadata.zip", package="Risa") armstrongISA <- readISAtab(zipfile = armstrongISAzip, path = file.path(system.file("extdata", package="Risa"),"armstrongISA"), verbose =TRUE) armstrongADF <- getAnnotatedDataFrameAssay(armstrongISA, [email protected][[1]]) str(armstrongADF)faahkoISAzip <- system.file("extdata","faahKO-metadata.zip", package="Risa") faahkoISA <- readISAtab(zipfile = faahkoISAzip, path = file.path(system.file("extdata", package="Risa"),"faahkoISA"), verbose =TRUE) faahkoADF <- getAnnotatedDataFrameAssay(faahkoISA, faahkoISA@assay.filenames[[1]]) str(faahkoADF) armstrongISAzip <- system.file("extdata","ARMSTRONG-S-3-metadata.zip", package="Risa") armstrongISA <- readISAtab(zipfile = armstrongISAzip, path = file.path(system.file("extdata", package="Risa"),"armstrongISA"), verbose =TRUE) armstrongADF <- getAnnotatedDataFrameAssay(armstrongISA, armstrongISA@assay.filenames[[1]]) str(armstrongADF)
getAssayRawDataFilenames in Package Risa ~~~~ Methods for function getAssayRawDataFilenames in package Risa ~~
They retrieve the raw data files for a particular assay type.
signature(.Object = "AssayTab", full.path = "logical")Retrieves the raw data filenames for a generic assay.
signature(.Object = "MicroarrayAssayTab", full.path = "logical")Retrieves the raw data filenames for an assay whose technology type is DNA microarray.
signature(.Object = "MSAssayTab", full.path = "logical")Retrieves the raw data filenames for an assay whose technology type is mass spectrometry. These data filenames correspond to those specified in the column 'Raw Spectral Data File'.
signature(.Object = "NMRAssayTab", full.path = "logical")Retrieves the raw data filenames for an assay whose technology type is NMR spectroscopy.
signature(.Object = "SeqAssayTab", full.path = "logical")Retrieves the raw data filenames for an assay whose technology type is nucleotide sequencing.
Retrieves an ExpressionSet for a DNA microarray assay.
getExpressionSet(isa, assay.filename)getExpressionSet(isa, assay.filename)
isa |
An object from the |
assay.filename |
A character vector with the assay filename of the microarray assay. |
It returns an ExpressionSet.
Alejandra Gonzalez-Beltran
affy
data.dir <- system.file("extdata", package="Risa") isazip <- system.file("extdata","ARMSTRONG-S-3-metadata.zip", package="Risa") path <- file.path(data.dir,"ARMSTRONG_ISA") isa <- readISAtab(zipfile = isazip, path = path, verbose =TRUE) path <- file.path(data.dir,"ARMSTRONG_ISA/") cel.files <- c("GSM510377_SA2006121413.CEL", "GSM510378_SA2006121414.CEL", "GSM510379_SA2006121415.CEL", "GSM510380_SA2006121416.CEL", "GSM510381_SA2006121417.CEL", "GSM510382_SA2006121418.CEL","GSM510383_SA2006121419.CEL","GSM510384_SA2006121420.CEL", "GSM510385_SA2006121421.CEL","GSM510386_SA2006121427.CEL", "GSM510387_SA2006121428.CEL", "GSM510388_SA2006121429.CEL", "GSM510389_SA2006121440.CEL","GSM510390_SA2006121441.CEL", "GSM510391_SA2006121442.CEL") base.url <- "http://perdera.sph.harvard.edu/biidata/microarray/study_ARMSTRONG-S-3_3Zd4KeJNJ7/raw_data/" ###########download all the cel files - this is commented out, uncomment the following two lines if you want to build the expression set #lapply(cel.files, function(x) download.file(paste(base.url, x, sep=""), destfile=paste(path, x, sep=""))) #getExpressionSet(isa, [email protected][[1]])data.dir <- system.file("extdata", package="Risa") isazip <- system.file("extdata","ARMSTRONG-S-3-metadata.zip", package="Risa") path <- file.path(data.dir,"ARMSTRONG_ISA") isa <- readISAtab(zipfile = isazip, path = path, verbose =TRUE) path <- file.path(data.dir,"ARMSTRONG_ISA/") cel.files <- c("GSM510377_SA2006121413.CEL", "GSM510378_SA2006121414.CEL", "GSM510379_SA2006121415.CEL", "GSM510380_SA2006121416.CEL", "GSM510381_SA2006121417.CEL", "GSM510382_SA2006121418.CEL","GSM510383_SA2006121419.CEL","GSM510384_SA2006121420.CEL", "GSM510385_SA2006121421.CEL","GSM510386_SA2006121427.CEL", "GSM510387_SA2006121428.CEL", "GSM510388_SA2006121429.CEL", "GSM510389_SA2006121440.CEL","GSM510390_SA2006121441.CEL", "GSM510391_SA2006121442.CEL") base.url <- "http://perdera.sph.harvard.edu/biidata/microarray/study_ARMSTRONG-S-3_3Zd4KeJNJ7/raw_data/" ###########download all the cel files - this is commented out, uncomment the following two lines if you want to build the expression set #lapply(cel.files, function(x) download.file(paste(base.url, x, sep=""), destfile=paste(path, x, sep=""))) #getExpressionSet(isa, [email protected][[1]])
If the assay.filename uses the microarray technology, it retrieves an object of the class MIAME with the minimum information about the experiment. Otherwise, it outputs a message indicating that the method is not valid for assays not using the microarray technology.
getMIAMEMetadata(isa, assay.filename)getMIAMEMetadata(isa, assay.filename)
isa |
An object of the |
assay.filename |
A string indicating the name of an assay file. It must correspond to a microarray-based assay for the function to return a valid value. |
It retrieves an object from the MIAME class or an error message.
Alejandra Gonzalez-Beltran
isMicroarrayAssay
armstrongISAzip <- system.file("extdata","ARMSTRONG-S-3-metadata.zip", package="Risa") armstrongISA <- readISAtab(zipfile = armstrongISAzip, path = file.path(system.file("extdata", package="Risa"),"armstrongISA"), verbose =TRUE) assay.filename <- [email protected][[1]] miame <- getMIAMEMetadata(armstrongISA, assay.filename) str(miame)armstrongISAzip <- system.file("extdata","ARMSTRONG-S-3-metadata.zip", package="Risa") armstrongISA <- readISAtab(zipfile = armstrongISAzip, path = file.path(system.file("extdata", package="Risa"),"armstrongISA"), verbose =TRUE) assay.filename <- armstrongISA@assay.filenames[[1]] miame <- getMIAMEMetadata(armstrongISA, assay.filename) str(miame)
Retrieves the list of asssay filenames in an ISAtab dataset, which correspond to microarray-based assays.
getMicroarrayAssayFilenames(isa)getMicroarrayAssayFilenames(isa)
isa |
An object of the |
a list of assay filenames
Alejandra Gonzalez-Beltran
isMicroarrayAssay
armstrongISAzip <- system.file("extdata","ARMSTRONG-S-3-metadata.zip", package="Risa") armstrongISA <- readISAtab(zipfile = armstrongISAzip, path = file.path(system.file("extdata", package="Risa"),"armstrongISA"), verbose =TRUE) getMicroarrayAssayFilenames(armstrongISA)armstrongISAzip <- system.file("extdata","ARMSTRONG-S-3-metadata.zip", package="Risa") armstrongISA <- readISAtab(zipfile = armstrongISAzip, path = file.path(system.file("extdata", package="Risa"),"armstrongISA"), verbose =TRUE) getMicroarrayAssayFilenames(armstrongISA)
Given an object from the ISAtab-class, this method retrieves a vector with the assay filenames corresponding to mass spectrometry (identified by having a column called 'Raw Spectral Data File'.
getMSAssayFilenames(isa)getMSAssayFilenames(isa)
isa |
an object from the ISAtab class |
A character vector with the assay filenames corresponding to mass spectrometry.
Alejandra Gonzalez-Beltran
data.dir <- system.file("extdata", package="Risa") isazip <- system.file("extdata","faahKO-metadata.zip", package="Risa") faahkoISA <- readISAtab(zipfile = isazip, path = file.path(data.dir,"faahKOISA"), verbose =TRUE) ms.assay.filenames <- getMSAssayFilenames(faahkoISA)data.dir <- system.file("extdata", package="Risa") isazip <- system.file("extdata","faahKO-metadata.zip", package="Risa") faahkoISA <- readISAtab(zipfile = isazip, path = file.path(data.dir,"faahKOISA"), verbose =TRUE) ms.assay.filenames <- getMSAssayFilenames(faahkoISA)
getRawDataFilenames in Package Risa ~~~~ Methods for function getRawDataFilenames in package Risa ~~\
To retrieve the raw data filenames in the ISATab dataset.
signature(.Object = "ISATab", full.path = "logical")Retrieves the raw data filenames in the ISATab dataset given an object from the ISATab-class and a boolean value indicating if the filenames are retrieved with their full path or not.
Retrieves the study filename to which an assay.filename corresponds.
getStudyFilename(isa, assay.filename)getStudyFilename(isa, assay.filename)
isa |
an object from the |
assay.filename |
a string with the filename of an assay |
a string with the study filename.
Alejandra Gonzalez-Beltran
ISATab-class
faahkoISA <- readISAtab(find.package("faahKO")) getStudyFilename(faahkoISA, [email protected][[1]])faahkoISA <- readISAtab(find.package("faahKO")) getStudyFilename(faahkoISA, faahkoISA@assay.filenames[[1]])
"ISATab", a class for maintaing ISATab informationThis class maintains information from an ISATab dataset, including an investigation file, one or more study files, and one or more assay files for each study file.
Objects can be created by calls of the form new("ISATab", ...).
path:Object of class "character", it represents the path of the ISA-Tab dataset
investigation.filename:Object of class "character", it represents the name of the Investigation file
investigation.file:Object of class "data.frame", it is a data frame with the contents of the Investigation file
investigation.identifier:Object of class "character", it is a string with the identifier for the investigation
study.identifiers:Object of class "character", it is the list of study identifiers
study.titles:Object of class "character", it is the list of study titles
study.descriptions:Object of class "character", it is the list of study descriptions
study.contacts:Object of class "character", it is the list of study contacts
study.contacts.affiliations:Object of class "character", it is the list of affiliations of the study contacts
study.filenames:Object of class "character", the names of the study files
study.files:Object of class "list", a list of data frames wiht the contents of the study files
assay.filenames:Object of class "character", the names of the assay files
assay.filenames.per.study:Object of class "list", the names of the assay files according to the study they belong to
assay.files:Object of class "list", a list of data frames with the contents of the assay files
assay.files.per.study:Object of class "list", a list of data frames with the contents of the assay files divided per study they belong to
assay.names:Object of class "list", which is a list of data frames, containing, per each assay file, the column of the assay file corresponding to the "Assay Name"
assay.technology.types:Object of class "character", a list with the technology types corresponding to each assay
assay.measurement.types:Object of class "character", a list with the names of the data files
data.filenames:Object of class "list", a list with the names of the samples
samples:Object of class "character"
samples.per.study:Object of class "list",
samples.per.assay.filename:Object of class "list",the samples classified according to the assay filename they belong to
assay.filenames.per.sample:Object of class "list", where each element is a list of assay file names per each sample name
sample.to.rawdatafile:Object of class "list", a list of data frames with samples associated with raw data files
sample.to.assayname:Object of class "list", maintains the association between samples and assay names
rawdatafile.to.sample:Object of class "list", mantains the association raw data file and samples
assayname.to.sample:Object of class "list", mantains the associations between assay names and samples
factors:Object of class "list", which contains R 'factor' objects for each of the studies (with factor names and factor levels).
treatments:Object of class "list" of data frames with the combination of factor values, per study file, or a factor object, if there is a single study
groups:Object of class "list", with one element per study file, and each element is a list of the samples for the corresponding treatment
assay.tabs:Object of class "list", where each element is an object of the class AssayTab or its specialisations (MSAssayTab or MicroarrayAssayTab), representing the information of each of the assay files in the investigation.
signature(x = "ISATab"): ...
signature(.Object="ISATab", full.path=TRUE): get the raw data filenames for all the assays in the ISATab dataset
No notes yet.
Alejandra Gonzalez-Beltran, [email protected]
Risa is a component of the ISA software infrastructure http://isa-tools.org/. The source code and latest version can be found in the GitHub repository https://github.com/ISA-tools/Risa. Please, submit all 'bugs' and feature requests through https://github.com/ISA-tools/Risa/issues.
ISATab-methods
showClass("ISATab")showClass("ISATab")
Retrieves a boolean value indicating wether the assay filename given as parameter corresponds to a microarray-based assay or not.
isMicroarrayAssay(isa, assay.filename)isMicroarrayAssay(isa, assay.filename)
isa |
An object of the |
assay.filename |
A string indicating the name of an assay file. It must correspond to a microarray-based assay for the function to return a valid value. |
Retrieves a boolean value.
Alejandra Gonzalez-Beltran
getMIAMEMetadata
data.dir <- system.file("extdata", package="Risa") isazip <- system.file("extdata","ARMSTRONG-S-3-metadata.zip", package="Risa") isa <- readISAtab(zipfile = isazip, path = file.path(data.dir,"ARMSTRONG_ISA"), verbose =TRUE) assay.filename <- [email protected][[1]] isMicroarrayAssay(isa, assay.filename)data.dir <- system.file("extdata", package="Risa") isazip <- system.file("extdata","ARMSTRONG-S-3-metadata.zip", package="Risa") isa <- readISAtab(zipfile = isazip, path = file.path(data.dir,"ARMSTRONG_ISA"), verbose =TRUE) assay.filename <- isa@assay.filenames[[1]] isMicroarrayAssay(isa, assay.filename)
Indicates if an assay filename corresponds to a mass spectrometry assay.
isMSAssay(isa, assay.filename)isMSAssay(isa, assay.filename)
isa |
an object from the ISAtab-class. |
assay.filename |
the filename of an assay file |
It retrieves a boolean value indicating wether the assay is a mass spectrometry assay or not.
Alejandra Gonzalez-Beltran
faahkoISA = readISAtab(find.package("faahKO")) assay.filename <- faahkoISA["assay.filenames"][[1]] isMSAssay(faahkoISA, assay.filename)faahkoISA = readISAtab(find.package("faahKO")) assay.filename <- faahkoISA["assay.filenames"][[1]] isMSAssay(faahkoISA, assay.filename)
processAssayXcmsSet retrieves an xcmsSet object given and ISA-tab object and one of its assay filenames.
processAssayXcmsSet(isa, assay.filename, ...)processAssayXcmsSet(isa, assay.filename, ...)
isa |
an ISA object, as retrieved by the function |
assay.filename |
a boolean indicating to show messages for the different steps, if TRUE, or not to show them, if FALSE |
... |
extra arguments that can be pass down to the xcmsSet function from the xcms package |
the xcmsSet object built from the assay metadata, considering all the factors defined, and data files
Steffen Neumann, Alejandra Gonzalez-Beltran / Maintainer: Alejandra Gonzalez-Beltran [email protected]
readISAtab
faahkoISA = readISAtab(find.package("faahKO")) assay.filename <- faahkoISA["assay.filenames"][[1]] xset = processAssayXcmsSet(faahkoISA, assay.filename)faahkoISA = readISAtab(find.package("faahKO")) assay.filename <- faahkoISA["assay.filenames"][[1]] xset = processAssayXcmsSet(faahkoISA, assay.filename)
processAssayXcmsSet.1factor retrieves an xcmsSet object given and ISA-tab object and one of its assay filenames.
processAssayXcmsSet.1factor(isa, assay.filename, ...)processAssayXcmsSet.1factor(isa, assay.filename, ...)
isa |
an ISA object, as retrieved by the function |
assay.filename |
a boolean indicating to show messages for the different steps, if TRUE, or not to show them, if FALSE |
... |
extra arguments that can be pass down to the xcmsSet function from the xcms package |
the xcmsSet object built from the assay metadata, considering all the factors defined, and data files
Alejandra Gonzalez-Beltran / Maintainer: Alejandra Gonzalez-Beltran [email protected]
readISAtab
faahkoISA = readISAtab(find.package("faahKO")) assay.filename <- faahkoISA["assay.filenames"][[1]] xset = processAssayXcmsSet.1factor(faahkoISA, assay.filename)faahkoISA = readISAtab(find.package("faahKO")) assay.filename <- faahkoISA["assay.filenames"][[1]] xset = processAssayXcmsSet.1factor(faahkoISA, assay.filename)
Reads an ISAtab dataset given as a zip file or as a set of files in a specific folder, and builds an object from the ISAtab class.
readISAtab(path = getwd(), zipfile = NULL, verbose = FALSE)readISAtab(path = getwd(), zipfile = NULL, verbose = FALSE)
path |
the name of the directory in which the ISAtab files are located (if the parameter zipfile is not provided or if it is equal to NULL), or the name of the directory where the zip file will be extracted (if the parameter zipfile is not NULL.) The default is the working directory. |
zipfile |
a zip archive containing ISAtab files. The default value is NULL. |
verbose |
a boolean indicating to show messages for the different steps, if TRUE, or not to show them, if FALSE |
The result is an object from the ISAtab class.
Alejandra Gonzalez-Beltran, Audrey Kauffmann / Maintainer: Alejandra Gonzalez-Beltran, ISA Team <[email protected]>
## Example for mass spectrometry dataset temp = tempdir() datafiles = c(file.path(system.file("cdf/KO", package="faahKO"), grep("CDF",dir(system.file("cdf/KO", package="faahKO")),ignore.case=TRUE,value=TRUE)), file.path(system.file("cdf/WT", package="faahKO"), grep("CDF",dir(system.file("cdf/WT", package="faahKO")),value=TRUE))) file.copy(datafiles, temp, recursive=TRUE) isafiles = file.path(system.file(package="faahKO"), grep("txt",dir(system.file(package="faahKO")),value=TRUE)) file.copy(isafiles, temp, recursive=TRUE) isaObject1 = readISAtab(path = temp) ## Example of readISAtab for a mass spectrometry experiment isazip <- system.file("extdata","faahKO-metadata.zip", package="Risa") isaObject2 <- readISAtab(zipfile = isazip, path = file.path(system.file("extdata", package="Risa"),"ISAexample"), verbose =TRUE)## Example for mass spectrometry dataset temp = tempdir() datafiles = c(file.path(system.file("cdf/KO", package="faahKO"), grep("CDF",dir(system.file("cdf/KO", package="faahKO")),ignore.case=TRUE,value=TRUE)), file.path(system.file("cdf/WT", package="faahKO"), grep("CDF",dir(system.file("cdf/WT", package="faahKO")),value=TRUE))) file.copy(datafiles, temp, recursive=TRUE) isafiles = file.path(system.file(package="faahKO"), grep("txt",dir(system.file(package="faahKO")),value=TRUE)) file.copy(isafiles, temp, recursive=TRUE) isaObject1 = readISAtab(path = temp) ## Example of readISAtab for a mass spectrometry experiment isazip <- system.file("extdata","faahKO-metadata.zip", package="Risa") isaObject2 <- readISAtab(zipfile = isazip, path = file.path(system.file("extdata", package="Risa"),"ISAexample"), verbose =TRUE)
The Risa package builds R objects from ISA-tab format files and it is a component of the ISA software infrastructure (see http://isa-tools.org/). ISA stands for Investigation, Study, Assay and the infrastructure revolves around the ISA-Tab format, which supports descriptions of biological experiments, with focus but not limited to high-throughput experiments. The format is supported by a series of open-source tools (all available in There is a growing international user community of the ISA infrastructure, featured in the ISA commons website (http://isacommons.org).
The source code and latest version of the Risa package can be found in the GitHub repository https://github.com/ISA-tools/Risa. Please, submit all 'bugs' and feature requests through https://github.com/ISA-tools/Risa/issues.
The function readISAtab reads ISA-tab files from a local zip archive or from a local folder.
The package also contains methods to save the ISA-tab files and to update the metadata after analysis. For mass spectrometry assays, the package includes several methods to build necessary object for processing using the xcms package (available in Bioconductor).
There are also functions to deal with DNA microarray-based assays, such as building an ExpressionSet object, relying on the affy package (available in Bioconductor)
In addition, there is a function called suggestBiocPackage that, given an object from the ISAtab-class - i.e. an ISAtab dataset - it will retrieve a list of potentially useful packages from Bioconductor, according to the assays measurement and technology types. This functionality is based on the annotations provided by the BiocViews.
The Risa package bridges the ISA metadata with analysis pipelines in R, and this is the reason of its name: R + ISA = Risa. Anecdotically, we note that Risa is the Pleasure Planet in Star Trek (see http://en.memory-alpha.org/wiki/Risa) and that 'Risa' means laughter in Spanish.
Alejandra Gonzalez-Beltran, Steffen Neumann, Audrey Kauffmann, Gabriella Rustici, Philippe Rocca-Serra, Eamonn Maguire, Susanna-Asunta Sansone. Maintainer: Alejandra Gonzalez-Beltran [email protected]
readISAtab, processAssayXcmsSet, updateAssayMetadata, write.ISAtab
## Example of readISAtab for a mass spectrometry experiment from a zip file isazip = system.file("extdata","faahKO-metadata.zip", package="Risa") isaset = readISAtab(zipfile = isazip, path = file.path(system.file("extdata", package="Risa"),"ISAexample"), verbose =TRUE) require("faahKO") ## Example of readISAtab for mass spectrometry data temp = tempdir() datafiles = c(file.path(system.file("cdf/KO", package="faahKO"), grep("CDF",dir(system.file("cdf/KO", package="faahKO")),value=TRUE)), file.path(system.file("cdf/WT", package="faahKO"), grep("CDF",dir(system.file("cdf/WT", package="faahKO")),value=TRUE))) file.copy(datafiles, temp, recursive=TRUE) isafiles = file.path(system.file(package="faahKO"), grep("txt",dir(system.file(package="faahKO")),value=TRUE)) file.copy(isafiles, temp, recursive=TRUE) isatab.object = readISAtab(path = temp)## Example of readISAtab for a mass spectrometry experiment from a zip file isazip = system.file("extdata","faahKO-metadata.zip", package="Risa") isaset = readISAtab(zipfile = isazip, path = file.path(system.file("extdata", package="Risa"),"ISAexample"), verbose =TRUE) require("faahKO") ## Example of readISAtab for mass spectrometry data temp = tempdir() datafiles = c(file.path(system.file("cdf/KO", package="faahKO"), grep("CDF",dir(system.file("cdf/KO", package="faahKO")),value=TRUE)), file.path(system.file("cdf/WT", package="faahKO"), grep("CDF",dir(system.file("cdf/WT", package="faahKO")),value=TRUE))) file.copy(datafiles, temp, recursive=TRUE) isafiles = file.path(system.file(package="faahKO"), grep("txt",dir(system.file(package="faahKO")),value=TRUE)) file.copy(isafiles, temp, recursive=TRUE) isatab.object = readISAtab(path = temp)
Suggest a list of packages available in Bioconductor, which may be useful for processing the assay according to its technology and measurement types.
suggestBiocPackage(isa,bioc.version)suggestBiocPackage(isa,bioc.version)
isa |
An |
bioc.version |
The version number of Bioconductor to be considered as the source of the pacakges for suggestions. |
Alejandra Gonzalez-Beltran
updateAssayMetadata Updates metadata into a particular assay file. See an example of use for a metabolite dataset at https://github.com/sneumann/mtbls2.
updateAssayMetadata(isa, assay.filename, col.name, values)updateAssayMetadata(isa, assay.filename, col.name, values)
isa |
An isatab object, as retrieved by the |
assay.filename |
the filename of the assay file to be augmented/modified |
col.name |
the name of the column of the assay file to be modified |
values |
the values to be added to the column of the assay file: it could be a single value, and in this case the value is repeated across the column, or it could be a list of values (whose length must match the number of rows of the assay file) |
The updated ISA-Tab object.
Alejandra Gonzalez-Beltran / Maintainer: Alejandra Gonzalez-Beltran, ISA Team <[email protected]>
readISAtab, https://github.com/sneumann/mtbls2
### This example shows how to add values to the column "Derived Spectral Data File", assuming that the results are stored in the file "faahkoDSDF.txt" faahkoISA = readISAtab(find.package("faahKO")) assay.filename <- faahkoISA["assay.filenames"][[1]] updateAssayMetadata(faahkoISA, assay.filename,"Derived Spectral Data File","faahkoDSDF.txt" )### This example shows how to add values to the column "Derived Spectral Data File", assuming that the results are stored in the file "faahkoDSDF.txt" faahkoISA = readISAtab(find.package("faahKO")) assay.filename <- faahkoISA["assay.filenames"][[1]] updateAssayMetadata(faahkoISA, assay.filename,"Derived Spectral Data File","faahkoDSDF.txt" )
write.assay.file writes a specific assay file from the ISA-tab dataset into disk.
write.assay.file(isa, assay.filename, path = getwd())write.assay.file(isa, assay.filename, path = getwd())
isa |
the ISA-Tab object (as retrieved by the readISAtab function ) |
assay.filename |
the name of the assay file to be written to disk |
path |
the output path in which the study file is going to be written, by default is the working directory |
Alejandra Gonzalez-Beltran / Maintainer: Alejandra Gonzalez-Beltran, ISA Team <[email protected]>
write.ISAtab,write.investigation.file, write.study.file, readISAtab
### Example of writing the study file of faahKO ISA-Tab dataset into the temp directory faahkoISA <- readISAtab(find.package("faahKO")) temp = tempdir() write.assay.file(faahkoISA, faahkoISA["assay.filenames"][[1]], temp)### Example of writing the study file of faahKO ISA-Tab dataset into the temp directory faahkoISA <- readISAtab(find.package("faahKO")) temp = tempdir() write.assay.file(faahkoISA, faahkoISA["assay.filenames"][[1]], temp)
write.investigation.file reads a ISA-tab file.
write.investigation.file(isa, path = getwd())write.investigation.file(isa, path = getwd())
isa |
the ISA-Tab object (as retrieved by the readISAtab function) |
path |
the output path in which the study file is going to be written, by default is the working directory |
Alejandra Gonzalez-Beltran / Maintainer: Alejandra Gonzalez-Beltran, ISA Team <[email protected]>
write.ISAtab, write.study.file, write.assay.file, readISAtab
### Example of writing the study file of faahKO ISA-Tab dataset into the temp director faahkoISA <- readISAtab(find.package("faahKO")) temp = tempdir() write.investigation.file(faahkoISA, temp)### Example of writing the study file of faahKO ISA-Tab dataset into the temp director faahkoISA <- readISAtab(find.package("faahKO")) temp = tempdir() write.investigation.file(faahkoISA, temp)
write.ISAtab writes a ISA-Tab dataset.
write.ISAtab(isa, path = getwd())write.ISAtab(isa, path = getwd())
isa |
the ISA-Tab object as built with the function |
path |
the directory where the files are going to be written, by default is the working directory |
Alejandra Gonzalez-Beltran / Maintainer: Alejandra Gonzalez-Beltran, ISA Team <[email protected]>
write.investigation.file, write.study.file, write.assay.file, readISAtab
### Example of writing the study file of faahKO ISA-Tab dataset into the temp director data.dir <- system.file("extdata", package="Risa") isazip <- system.file("extdata","faahKO-metadata.zip", package="Risa") faahkoISA <- readISAtab(zipfile = isazip, path = file.path(data.dir,"faahKOISA"), verbose =TRUE) temp = tempdir() write.ISAtab(faahkoISA, temp)### Example of writing the study file of faahKO ISA-Tab dataset into the temp director data.dir <- system.file("extdata", package="Risa") isazip <- system.file("extdata","faahKO-metadata.zip", package="Risa") faahkoISA <- readISAtab(zipfile = isazip, path = file.path(data.dir,"faahKOISA"), verbose =TRUE) temp = tempdir() write.ISAtab(faahkoISA, temp)
write.study.file writes a specific Study file from the ISA-tab dataset.
write.study.file(isa, study.filename, path = getwd())write.study.file(isa, study.filename, path = getwd())
isa |
the ISA-Tab object (as retrieved by the readISAtab function) |
study.filename |
the name of the study file to be written to disk |
path |
the output path in which the study file is going to be written, by default is the working directory |
Alejandra Gonzalez-Beltran / Maintainer: Alejandra Gonzalez-Beltran, ISA Team <[email protected]>
write.study.file, write.ISAtab, readISAtab
### Example of writing the study file of faahKO ISA-Tab dataset into the temp director faahkoISA <- readISAtab(find.package("faahKO")) temp = tempdir() write.study.file(faahkoISA, faahkoISA["study.filenames"][[1]], temp)### Example of writing the study file of faahKO ISA-Tab dataset into the temp director faahkoISA <- readISAtab(find.package("faahKO")) temp = tempdir() write.study.file(faahkoISA, faahkoISA["study.filenames"][[1]], temp)