I want to download the sample information of a 450k methylation array dataset (GSE49031). However, when I try to do so with the R code below I automatically also download and parse a 213.4 MB soft file with the platform information, including annotations for the 485577 probes. This takes a long time and I am not interested in doing it. Is there a way to only get the sample information?
gse <- getGEO("GSE49031", destdir="data")
I tried to be clever and downloaded the series information manually prior to parsing (which is only 24.8 kB), but
getGEO still went online and downloaded the platform information.
in.file <- "data/GSE49031_series_matrix.txt.gz" download.file("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49031/matrix/GSE49031_series_matrix.txt.gz", in.file) gse <- getGEO(filename=in.file, destdir="data")
I have read the manual and searched for a solution online, but cannot figure out how to do it.