summarizeGEOSoft | R Documentation |
takes as input the list returned by parseGEOSoft
,
a GEO microarray data set, including a table of probe mappings,
as provided via GEO soft family files.
Argument id
specifies a probe mapping column ID.
Multiples probes for the same features (same string in column ID) will
then be summarized by the function in argument avg
(default: median). If the package farms installed, the more
sophisticated probe summarization of this package can be used
https://www.bioconductor.org/packages/release/bioc/html/farms.html.
summarizeGEOSoft(
data,
id = "ORF",
avg = "mean",
farms = FALSE,
keep.empty = FALSE,
replicate = FALSE,
repsep = ";",
verb = TRUE,
...
)
data |
a list as returned by function |
id |
a column ID; probes with equal strings in this column will be summarized |
avg |
a function (or the name of a function as a string)
for calculating an ‘average’ value for each cluster; default is
the |
farms |
logical to indicate to use the bioconductor package
farms for probe summarization (function |
keep.empty |
keep columns with no entry in column ID by copying the probe ID |
replicate |
if TRUE probe sets assigned to multiple features (separated by string provided in rep.sep) will be duplicated to and each feature will get its own row |
repsep |
separator for multiple-feature probes |
verb |
print messages |
... |
arguments to the function specified in |
parseGEOSoft
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