| Title: | Loading and annotation RNA-seq counts matrices |
|---|---|
| Description: | PhantasusLite – a lightweight package with helper functions of general interest extracted from phantasus package. In parituclar it simplifies working with public RNA-seq datasets from GEO by providing access to the remote HSDS repository with the precomputed gene counts from ARCHS4 and DEE2 projects. |
| Authors: | Rita Sablina [aut], Maxim Kleverov [aut], Alexey Sergushichev [aut, cre] |
| Maintainer: | Alexey Sergushichev <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.5.0 |
| Built: | 2024-11-18 03:54:55 UTC |
| Source: | https://github.com/bioc/phantasusLite |
Returns list of all HDF5-files on HSDS-server
getHSDSFileList( url = "https://alserglab.wustl.edu/hsds/?domain=/counts", directory = NULL )getHSDSFileList( url = "https://alserglab.wustl.edu/hsds/?domain=/counts", directory = NULL )
url |
containing url of the server and root domain. |
directory |
containing name of the directory |
List of all HDF5-files on the server or all files of the collection
url <- 'https://alserglab.wustl.edu/hsds/?domain=/counts' getHSDSFileList(url)url <- 'https://alserglab.wustl.edu/hsds/?domain=/counts' getHSDSFileList(url)
Adds condition to the annotation.
inferCondition(es)inferCondition(es)
es |
contains ExpressionSet object |
Annotated ExpressionSet with conditions and replicates
ess <- GEOquery::getGEO("GSE143903") es <- ess[[1]] es <- inferCondition(es) es$condition # contains inferred groups es$replicate # contains inferred replicate numbersess <- GEOquery::getGEO("GSE143903") es <- ess[[1]] es <- inferCondition(es) es$condition # contains inferred groups es$replicate # contains inferred replicate numbers
Load count matrix from remote HDF5-file
loadCountsFromH5FileHSDS( es, url = "https://alserglab.wustl.edu/hsds/?domain=/counts", file, sampleIndexes = NULL )loadCountsFromH5FileHSDS( es, url = "https://alserglab.wustl.edu/hsds/?domain=/counts", file, sampleIndexes = NULL )
es |
containing ExpressionSet loaded from GEO. Contains empty expression matrix. |
url |
containing url of the server and root domain. |
file |
containing name of the file (relative to the root domain) |
sampleIndexes |
containing sample indexes list |
ExpressionSet object with loaded count matrix
ess <- GEOquery::getGEO("GSE53053") es <- ess[[1]] url <- 'https://alserglab.wustl.edu/hsds/?domain=/counts' file <- "/dee2/mmusculus_star_matrix_20240409.h5" es <- loadCountsFromH5FileHSDS(es, url, file)ess <- GEOquery::getGEO("GSE53053") es <- ess[[1]] url <- 'https://alserglab.wustl.edu/hsds/?domain=/counts' file <- "/dee2/mmusculus_star_matrix_20240409.h5" es <- loadCountsFromH5FileHSDS(es, url, file)
Load count matrix from HDF5-files.
loadCountsFromHSDS( es, url = "https://alserglab.wustl.edu/hsds/?domain=/counts" )loadCountsFromHSDS( es, url = "https://alserglab.wustl.edu/hsds/?domain=/counts" )
es |
containing ExpressionSet loaded from GEO. Contains empty expression matrix. |
url |
containing url of the server and root domain. |
ExpressionSet with loaded count matrix
ess <- GEOquery::getGEO("GSE85653") es <- ess[[1]] url <- 'https://alserglab.wustl.edu/hsds/?domain=/counts' es <- loadCountsFromHSDS(es, url)ess <- GEOquery::getGEO("GSE85653") es <- ess[[1]] url <- 'https://alserglab.wustl.edu/hsds/?domain=/counts' es <- loadCountsFromHSDS(es, url)
Only versions 1.2 and 1.3 are supported.
readGct(gct)readGct(gct)
gct |
Path to gct file |
ExpressionSet object
es <- readGct(system.file("extdata/testdata/gct/test.gct", package="phantasusLite"))es <- readGct(system.file("extdata/testdata/gct/test.gct", package="phantasusLite"))
Saves ExpressionSet to a GCT file (version 1.3).
writeGct(es, file, gzip = FALSE)writeGct(es, file, gzip = FALSE)
es |
ExpresionSet obeject to save |
file |
Path to output gct file |
gzip |
Whether to gzip apply gzip-compression for the output file#' |
Result of the closing file (as in 'close()' function')
es <- readGct(system.file("extdata/testdata/gct/test.gct", package="phantasusLite")) out <- tempfile(fileext = ".gct.gz") writeGct(es, out, gzip=TRUE)es <- readGct(system.file("extdata/testdata/gct/test.gct", package="phantasusLite")) out <- tempfile(fileext = ".gct.gz") writeGct(es, out, gzip=TRUE)