bioconductor v3.9.0 GEOquery
The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.
Link to this section Summary
Functions
Class "GDS"
Class "GEODataTable"
Generic functions for GEOquery
Class "GEOData"
Class "GPL"
Class "GSE"
Class "GSM"
Convert a GDS data structure to a BioConductor data structure
get a directory listing from NCBI GEO
Get a GEO object from NCBI or file
Get Supplemental Files from GEO
Download a file from GEO soft file to the local machine
Get GSE data tables from GEO into R data structures.
Gunzip a file
Parse GEO text
Parse a GSE mstrix file
Link to this section Functions
GDS_class()
Class "GDS"
Description
A class describing a GEO GDS entity
Seealso
Author
Sean Davis
GEODataTable_class()
Class "GEODataTable"
Description
Contains the column descriptions and data for the datatable part of a GEO object
Author
Sean Davis
GEOData_accessors()
Generic functions for GEOquery
Description
The main documentation is in the Class documentation
Seealso
Author
Sean Davis
GEOData_class()
Class "GEOData"
Description
A virtual class for holding GEO samples, platforms, and datasets
Seealso
GDS-class , GPL-class ,
GSM-class , GEODataTable-class ,
Author
Sean Davis
GPL_class()
Class "GPL"
Description
Contains a full GEO Platform entity
Seealso
Author
Sean Davis
GSE_class()
Class "GSE"
Description
Contains a GEO Series entity
Seealso
Author
Sean Davis
GSM_class()
Class "GSM"
Description
A class containing a GEO Sample entity
Seealso
Author
Sean Davis
coercion()
Convert a GDS data structure to a BioConductor data structure
Description
Functions to take a GDS data structure from getGEO and coerce it to limma MALists or ExpressionSets.
Arguments
| Argument | Description |
|---|---|
GDS | The GDS datastructure returned by getGEO |
do.log2 | Boolean, should the data in the GDS be log2 transformed before inserting into the new data structure |
GPL | Either a GPL data structure (from a call to getGEO) or NULL. If NULL, this will cause a call to getGEO to produce a GPL. The gene information from the GPL is then used to construct the genes slot of the resulting limma MAList object or the featureData slot of the ExpressionSet instance. |
AnnotGPL | In general, the annotation GPL files will be available for GDS records, so the default is to use these files over the user-submitted GPL files |
getGPL | A boolean defaulting to TRUE as to whether or not to download and include GPL information when converting to ExpressionSet or MAList. You may want to set this to FALSE if you know that you are going to annotate your featureData using Bioconductor tools rather than relying on information provided through NCBI GEO. Download times can also be greatly reduced by specifying FALSE. |
Details
This function just rearranges one data structure into another. For GDS, it also deals appropriately with making the "targets" list item for the limma data structure and the phenoData slot of ExpressionSets.
Value
*
Author
Sean Davis
References
See the limma and ExpressionSet help in the appropriate packages
Examples
gds505 <- getGEO('GDS505')
MA <- GDS2MA(gds505)
eset <- GDS2eSet(gds505)getDirListing()
get a directory listing from NCBI GEO
Description
This one makes some assumptions about the structure of the HTML response returned.
Usage
getDirListing(url)Arguments
| Argument | Description |
|---|---|
url | A URL, assumed to return an NCBI-formatted index page |
getGEO()
Get a GEO object from NCBI or file
Description
This function is the main user-level function in the GEOquery package. It directs the download (if no filename is specified) and parsing of a GEO SOFT format file into an R data structure specifically designed to make access to each of the important parts of the GEO SOFT format easily accessible.
Usage
getGEO(GEO = NULL, filename = NULL, destdir = tempdir(),
GSElimits = NULL, GSEMatrix = TRUE, AnnotGPL = FALSE, getGPL = TRUE,
parseCharacteristics = TRUE)Arguments
| Argument | Description |
|---|---|
GEO | A character string representing a GEO object for download and parsing. (eg., 'GDS505','GSE2','GSM2','GPL96') |
filename | The filename of a previously downloaded GEO SOFT format file or its gzipped representation (in which case the filename must end in .gz). Either one of GEO or filename may be specified, not both. GEO series matrix files are also handled. Note that since a single file is being parsed, the return value is not a list of esets, but a single eset when GSE matrix files are parsed. |
destdir | The destination directory for any downloads. Defaults to the architecture-dependent tempdir. You may want to specify a different directory if you want to save the file for later use. Doing so is a good idea if you have a slow connection, as some of the GEO files are HUGE! |
GSElimits | This argument can be used to load only a contiguous subset of the GSMs from a GSE. It should be specified as a vector of length 2 specifying the start and end (inclusive) GSMs to load. This could be useful for splitting up large GSEs into more manageable parts, for example. |
GSEMatrix | A boolean telling GEOquery whether or not to use GSE Series Matrix files from GEO. The parsing of these files can be many orders-of-magnitude faster than parsing the GSE SOFT format files. Defaults to TRUE, meaning that the SOFT format parsing will not occur; set to FALSE if you for some reason need other columns from the GSE records. |
AnnotGPL | A boolean defaulting to FALSE as to whether or not to use the Annotation GPL information. These files are nice to use because they contain up-to-date information remapped from Entrez Gene on a regular basis. However, they do not exist for all GPLs; in general, they are only available for GPLs referenced by a GDS |
getGPL | A boolean defaulting to TRUE as to whether or not to download and include GPL information when getting a GSEMatrix file. You may want to set this to FALSE if you know that you are going to annotate your featureData using Bioconductor tools rather than relying on information provided through NCBI GEO. Download times can also be greatly reduced by specifying FALSE. |
parseCharacteristics | A boolean defaulting to TRUE as to whether or not to parse the characteristics information (if available) for a GSE Matrix file. Set this to FALSE if you experience trouble while parsing the characteristics. |
Details
getGEO functions to download and parse information available from NCBI GEO ( http://www.ncbi.nlm.nih.gov/geo ). Here are some details about what is avaible from GEO. All entity types are handled by getGEO and essentially any information in the GEO SOFT format is reflected in the resulting data structure.
From the GEO website:
The Gene Expression Omnibus (GEO) from NCBI serves as a public repository for a wide range of high-throughput experimental data. These data include single and dual channel microarray-based experiments measuring mRNA, genomic DNA, and protein abundance, as well as non-array techniques such as serial analysis of gene expression (SAGE), and mass spectrometry proteomic data. At the most basic level of organization of GEO, there are three entity types that may be supplied by users: Platforms, Samples, and Series. Additionally, there is a curated entity called a GEO dataset.
A Platform record describes the list of elements on the array (e.g., cDNAs, oligonucleotide probesets, ORFs, antibodies) or the list of elements that may be detected and quantified in that experiment (e.g., SAGE tags, peptides). Each Platform record is assigned a unique and stable GEO accession number (GPLxxx). A Platform may reference many Samples that have been submitted by multiple submitters.
A Sample record describes the conditions under which an individual Sample was handled, the manipulations it underwent, and the abundance measurement of each element derived from it. Each Sample record is assigned a unique and stable GEO accession number (GSMxxx). A Sample entity must reference only one Platform and may be included in multiple Series.
A Series record defines a set of related Samples considered to be part of a group, how the Samples are related, and if and how they are ordered. A Series provides a focal point and description of the experiment as a whole. Series records may also contain tables describing extracted data, summary conclusions, or analyses. Each Series record is assigned a unique and stable GEO accession number (GSExxx).
GEO DataSets (GDSxxx) are curated sets of GEO Sample data. A GDS record represents a collection of biologically and statistically comparable GEO Samples and forms the basis of GEO's suite of data display and analysis tools. Samples within a GDS refer to the same Platform, that is, they share a common set of probe elements. Value measurements for each Sample within a GDS are assumed to be calculated in an equivalent manner, that is, considerations such as background processing and normalization are consistent across the dataset. Information reflecting experimental design is provided through GDS subsets.
Value
An object of the appropriate class (GDS, GPL, GSM, or GSE) is returned. If the GSEMatrix option is used, then a list of ExpressionSet objects is returned, one for each SeriesMatrix file associated with the GSE accesion. If the filename argument is used in combination with a GSEMatrix file, then the return value is a single ExpressionSet.
Seealso
Author
Sean Davis
Examples
gds <- getGEO("GDS10")
gds
gse <- getGEO('GSE10')
# Returns a list, so look at first item
gse[[1]]getGEOSuppFiles()
Get Supplemental Files from GEO
Description
NCBI GEO allows supplemental files to be attached to GEO Series (GSE), GEO platforms (GPL), and GEO samples (GSM). This function "knows" how to get these files based on the GEO accession. No parsing of the downloaded files is attempted, since the file format is not generally knowable by the computer.
Usage
getGEOSuppFiles(GEO, makeDirectory = TRUE, baseDir = getwd(),
fetch_files = TRUE, filter_regex = NULL)Arguments
| Argument | Description |
|---|---|
GEO | A GEO accession number such as GPL1073 or GSM1137 |
makeDirectory | Should a "subdirectory" for the downloaded files be created? Default is TRUE. If FALSE, the files will be downloaded directly into the baseDir. |
baseDir | The base directory for the downloads. Default is the current working directory. |
fetch_files | logical(1). If TRUE, then actually download the files. If FALSE, just return the filenames that would have been downloaded. Useful for testing and getting a list of files without actual download. |
filter_regex | A character(1) regular expression that will be used to filter the filenames from GEO to limit those files that will be downloaded. This is useful to limit to, for example, bed files only. |
Details
Again, just a note that the files are simply downloaded.
Value
If fetch_files=TRUE, a data frame is returned invisibly with rownames representing the full path of the resulting downloaded files and the records in the data.frame the output of file.info for each downloaded file. If fetch_files=FALSE, a data.frame of URLs and filenames is returned.
Author
Sean Davis sdavis2@mail.nih.gov
Examples
a <- getGEOSuppFiles('GSM1137', fetch_files = FALSE)
agetGEOfile()
Download a file from GEO soft file to the local machine
Description
This function simply downloads a SOFT format file associated with the GEO accession number given.
Usage
getGEOfile(GEO, destdir = tempdir(), AnnotGPL = FALSE, amount = c("full",
"brief", "quick", "data"))Arguments
| Argument | Description |
|---|---|
GEO | Character string, the GEO accession for download (eg., GDS84, GPL96, GSE2553, or GSM10) |
destdir | Directory in which to store the resulting downloaded file. Defaults to tempdir() |
AnnotGPL | A boolean defaulting to FALSE as to whether or not to use the Annotation GPL information. These files are nice to use because they contain up-to-date information remapped from Entrez Gene on a regular basis. However, they do not exist for all GPLs; in general, they are only available for GPLs referenced by a GDS |
amount | Amount of information to pull from GEO. Only applies to GSE, GPL, or GSM. See details... |
Details
This function downloads GEO SOFT files based on accession number. It does not do any parsing. The first two arguments should be fairly self-explanatory, but the last is based on the input to the acc.cgi url at the geo website. In the default "full" mode, the entire SOFT format file is downloaded. Both "brief" and "quick" offer shortened versions of the files, good for "peeking" at the file before a big download on a slow connection. Finally, "data" downloads only the data table part of the SOFT file and is good for downloading a simple EXCEL-like file for use with other programs (a convenience).
Value
Invisibly returns the full path of the downloaded file.
Seealso
Author
Sean Davis
References
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi
Examples
# myfile <- getGEOfile('GDS10')getGSEDataTables()
Get GSE data tables from GEO into R data structures.
Description
In some cases, instead of individual sample records (GSM) containing
information regarding sample phenotypes, the GEO Series contains that
information in an attached data table. And example is given by GSE3494
where there are two data tables with important information contained within
them. Using getGEO with the standard parameters downloads the GSEMatrix
file which, unfortunately, does not contain the information in the data
tables. This function simply downloads the header'' information from the GSE record and parses out the data tables into R data.frames. ## Usage ```r getGSEDataTables(GSE) ``` ## Arguments |Argument |Description| |------------- |----------------| |`GSE` | The GSE identifier, such asGSE3494''.|
Value
A list of data.frames.
Seealso
Author
Sean Davis sdavis2@mail.nih.gov
Examples
dfl = getGSEDataTables("GSE3494")
lapply(dfl,head)gunzip()
Gunzip a file
Description
gunzip a file
Usage
gunzip(filename, destname = gsub("[.]gz$", "", filename), overwrite = FALSE,
remove = TRUE, BFR.SIZE = 1e+07)Arguments
| Argument | Description |
|---|---|
filename | The filename to be unzipped |
destname | The destination file |
overwrite | Boolean indicating whether or not to overwrite a destfile of the same name |
remove | Boolean indicating whether or not to remove the original file after completion |
BFR.SIZE | The size of the read buffer.... |
Details
This function was stripped out of R.utils due to breaking some stuff on the bioconductor build machine.
Value
Invisibly, the number of bytes read.
Seealso
Author
Original author: Henrik Bengtsson
Examples
# gunzip('file.gz',remove=FALSE)parseGEO()
Parse GEO text
Description
Workhorse GEO parsers.
Usage
parseGEO(fname, GSElimits, destdir = tempdir(), AnnotGPL = FALSE,
getGPL = TRUE)Arguments
| Argument | Description |
|---|---|
fname | The filename of a SOFT format file. If the filename ends in .gz, a gzfile() connection is used to read the file directly. |
GSElimits | Used to limit the number of GSMs parsed into the GSE object; useful for memory management for large GSEs. |
destdir | The destination directory into which files will be saved (to be used for caching) |
AnnotGPL | Fetch the annotation GPL if available |
getGPL | Fetch the GPL associated with a GSEMatrix entity (should remain TRUE for all normal use cases) |
Details
These are probably not useful to the end-user. Use getGEO to access these functions. parseGEO simply delegates to the appropriate specific parser. There should be no reason to use the parseGPL, parseGDS, parseGSE, or parseGSM functions directly.
Value
parseGEO returns an object of the associated type. For example, if it is passed the text from a GDS entry, a GDS object is returned.
Seealso
Author
Sean Davis
parseGSEMatrix()
Parse a GSE mstrix file
Description
Not meant for user calling, but parses a single GSEMatrix file.
Usage
parseGSEMatrix(fname, AnnotGPL = FALSE, destdir = tempdir(),
getGPL = TRUE, parseCharacteristics = TRUE)Arguments
| Argument | Description |
|---|---|
fname | filename |
AnnotGPL | set to TRUE to get the annotation GPL version |
destdir | the destdination directory for download |
getGPL | whether or not to get the GPL associated |
parseCharacteristics | Whether or not to do full "characteristic" parsing |