Get GSE data tables from GEO into R data structures.

In some cases, instead of individual sample records (GSM) containing information regarding sample phenotypes, the GEO Series contains that information in one or more data tables attached at the Series level. An example is given by GSE3494, where there are two data tables with important information contained within them. Series-level per-cell annotation tables from single-cell studies (the !series_table blocks in SOFT format, e.g. the "Listing of Individual Cells" table in GSE98638) are exposed here as well. 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

getGSEDataTables(GSE)

Arguments

GSE

The GSE identifier, such as “GSE3494”.

Value

A list of data.frames, one per <Data-Table> in the Series record (a Series may carry zero, one, or several). Each data.frame's column names are taken from the table's column definitions.

See also

getGEO

Author

Sean Davis sdavis2@mail.nih.gov

Examples

if (FALSE) { # \dontrun{

dfl = getGSEDataTables('GSE3494')
lapply(dfl,head)


} # }