Description Usage Arguments Details Value Author(s) See Also Examples
Given the identifier of a GEO series (GSE) record
creates one or more ExpressionSet
s from the data loaded in the compendium
database
1 | createESET(con, GSEid, GPLid = "", parsing = TRUE)
|
con |
|
GSEid |
character string specifying the GSE ID to be converted to one or more ExpressionSets |
GPLid |
character string specifying the GPL ID. The default value is
|
parsing |
logical, if set to its default value ( |
This function generates one or more ExpressionSets for the
specified GSE from the data loaded in the compendium database. Each
ExpressionSet
contains an assayData
slot with
all data related to the expression measurements parsed from a GSE SOFT
file. Probe annotation is provided in the featureData
slot with
all data parsed from the most recent annotation file provided for
the corresponding GPL (if available at
ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/annotation/platforms/).
Sample annotation is provided in the
phenoData
slot and obtained by parsing the output of the
function GSMdescriptions
.
A list
with components of class ExpressionSet
(from the Biobase
Bioconductor package). Each ExpressionSet
is named according to
the GSEid
with its corresponding GPL ID(s). If a GSE
consists of GSMs with a different number of features, multiple
ExpressionSets are created such that GSMs with the same features are
grouped into one ExpressionSet.
Umesh K. Nandal
GSMdescriptions
, updatePhenoData
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## Not run:
conn <- connectDatabase(dbname="compendium")
# Create ExpressionSet for the samples in GSE1657 corresponding to GPL96
esets <- createESET(conn,"GSE1657","GPL96")
# esets contains one component: "esetGSE1657_GPL96_SC"
# Create ExpressionSet for the samples of both platforms present in GSE1657 (GPL96 &
# GPL97), i.e, set GPLid to default value
esets <- createESET(conn,"GSE1657") # Default GPLid=""
# esets contains two components: "esetGSE1657_GPL96_SC" and "esetGSE1657_GPL97_SC"
## End(Not run)
|
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