A tool for efficiently grabbing usable metadata and experiment data off GEO for use in R.
Metadata by experiment accession number can be returned for all GEO experiments or by GPL platform code
devtools::load_all("~/repos/geograbi")
require("XML")## all datasets in GEO
datasets <- geograbi.retrieve.datasets() ## about 4min## all Illumina Infinium 27K DNA methylation datasets
datasets <- geograbi.retrieve.datasets(gpl = c("GPL13534")) ## 5sec> Thu Jan 17 14:47:24 2019 retrieving dataset UID 1 ...
> Thu Jan 17 14:47:30 2019 retrieved 1192
str(datasets)> 'data.frame': 1192 obs. of 9 variables:
> $ title : chr "Epigenome analysis of depressed and control subjects." "DNA methylation analysis in familial adenomatous polyposis" "Genome-Wide DNA Methylation Profiling of Oesophageal Cancer-Associated Myofibroblasts" "Genome-Wide DNA Methylation Profiling of Gastric Cancer-Associated Myofibroblasts" ...
> $ description: chr "Genome wide DNA methylation profiling of depressed (n=489) and control subjects (n=210) that were recruited at the Max Planck "| __truncated__ "DNA methylation of 23 familial adenomatous polyposis tumors. Infinium HumanMethylation450 BeadChip was used to obtain DNA methy"| __truncated__ "The Illumina Infinium HumanMethylation450 BeadChip arrays were performed on a collection of primary oesophageal cancer-associat"| __truncated__ "The Illumina Infinium HumanMethylation450 BeadChip arrays were performed on a collection of primary gastric cancer-associated m"| __truncated__ ...
> $ organism : chr "Homo sapiens" "Homo sapiens" "Homo sapiens" "Homo sapiens" ...
> $ type : chr "Methylation profiling by genome tiling array" "Methylation profiling by array" "Methylation profiling by array" "Methylation profiling by array" ...
> $ platform : chr "GPL13534" "GPL13534" "GPL13534" "GPL13534" ...
> $ accession : chr "GSE125105" "GSE109507" "GSE97687" "GSE97686" ...
> $ id : chr "200125105" "200109507" "200097687" "200097686" ...
> $ project : chr "" "" "" "" ...
> $ samples : int 699 23 10 9 55 60 329 22 148 138 ...
## by individual gses
filenames <- geograbi.download.series.files(gses = "GSE94734")
## or for a vector of gses
filenames <- geograbi.download.series.files(gses = datasets$accession[1:6])samples <- geograbi.get.samples(filename = "GSE94734_series_matrix.txt.gz")
gses <- lapply(na.omit(filenames), geograbi.get.samples)Automatically saves data to .rdata format at user-defined path
dat <- geograbi.get.data(filename = "GSE94734_series_matrix.txt.gz")Just the sample data
samples <- geograbi.get.samples("GSE94734")Just the experiment data
dat <- geograbi.get.data("GSE94734")Both the sample and experiment data at the same time
dataset <- geograbi.read.gse.matrix("GSE94734")names(dataset)> [1] "data" "samples" "series"
dim(dataset$samples)> [1] 178 46
dim(dataset$data)> [1] 485578 178