| Encoding: | UTF-8 |
| Title: | Easily Downloads a Gene Expression Dataset from a GEO Code and Retrieves the Gene Symbols of Its Probesets |
| Version: | 1.2 |
| Description: | A function that reads in the GEO code of a gene expression dataset, retrieves its data from GEO, (optionally) retrieves the gene symbols of the dataset, and returns a simple dataframe table containing all the data. Platforms available: GPL11532, GPL23126, GPL6244, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL https://ftp.ncbi.nlm.nih.gov/geo/series/. More information can be found in the following manuscript: Davide Chicco, "geneExpressionFromGEO: an R package to facilitate data reading from Gene Expression Omnibus (GEO)". Microarray Data Analysis, Methods in Molecular Biology, volume 2401, chapter 12, pages 187-194, Springer Protocols, 2021, <doi:10.1007/978-1-0716-1839-4_12>. |
| BugReports: | https://github.com/davidechicco/geneExpressionFromGEO/issues |
| Depends: | R (≥ 3.1.0) |
| License: | GPL-3 |
| URL: | https://github.com/davidechicco/geneExpressionFromGEO |
| Imports: | xml2, Biobase, annotate, GEOquery, qpdf |
| Suggests: | knitr, rmarkdown |
| VignetteBuilder: | knitr |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | no |
| Packaged: | 2025-04-11 09:50:54 UTC; davide |
| Author: | Davide Chicco 
[aut, cre] |
| Maintainer: | Davide Chicco <davidechicco@davidechicco.it> |
| Repository: | CRAN |
| Date/Publication: | 2025-04-11 12:00:05 UTC |
Function that returns numeric values with 2 decimal numbers.
Description
Function that returns numeric values with 2 decimal numbers.
Usage
dec_two(x)
Arguments
x |
input numeric value with N decimal numbers. |
Value
a numeric value with 2 decimal numbers.
Examples
aaa <- dec_two(8.31232)
Function that reads in the GEO code of a dataset, and returns the gene expression dataframe.
Description
Function that reads in the GEO code of a dataset, and returns the gene expression dataframe.
Usage
getGeneExpressionFromGEO(datasetGeoCode, retrieveGeneSymbols, verbose = FALSE)
Arguments
datasetGeoCode |
the GEO code of a dataset. |
retrieveGeneSymbols |
a boolean flag stating if the function should retrieve the gene symbols or not. |
verbose |
a boolean flag stating if helping messages should be printed or not |
Value
a gene expression dataset.
Examples
geneExpressionDF1 <- getGeneExpressionFromGEO("GSE47018", FALSE, FALSE)
Function that reads in a URL to check and verifies if it exists (function written by Janko Thyson @rappster and taken from https://stackoverflow.com/a/12195574 )
Description
Function that reads in a URL to check and verifies if it exists (function written by Janko Thyson @rappster and taken from https://stackoverflow.com/a/12195574 )
Usage
readUrl(url)
Arguments
url |
the URL of a webpage |
Value
the output of a webpage verification check
Examples
y <- readUrl("http://stat.ethz.ch/R-manual/R-devel/library/base/html/connections.html")