Description Usage Arguments Value Examples
Fetch expression data from GEO / or given folder
1 2 3 4 |
geo.id |
GEO id |
sample.mapping.column |
The column in the sample annotation that contains phenotype info (default: "characteristics_ch1") |
do.log2 |
Apply log2 transformation to the expression values. If NULL (default), deduced from the data (code from GEO2R at NCBI) |
probe.conversion |
Convert probe level expression to gene level using provided annotation label (uses platform specific annotations downloaded from GEO) Defaults to NULL (no conversion). In case of multiple probes, probe with absolute max value is chosen |
conversion.mapping |
Mapping of platform specific ids to user provided ids |
conversion.mapping.function |
Function to process the mapped name such that it matches with the ids provided in conversion.map |
output.dir |
Directory where all files will be written (defaults to current working dir) |
geo.id.sub |
GEO id for the sub-set (e.g., specific to the platform) |
A list containing 3 data frames: expression matrix, sample mapping, gene mapping
1 2 3 | gds.data = fetch.expression.data("GDS4966", do.log2=F, probe.conversion="Gene ID")
expr = gds.data$expr
sample.mapping = gds.data$sample.mapping
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