HyperGResult-accessors {Category} | R Documentation |
This manual page documents generic functions for extracting data
from the result object returned from a call to hyperGTest
.
The result object will be a subclass of HyperGResultBase
.
Methods apply to all result object classes unless otherwise noted.
pvalues(r) oddsRatios(r) expectedCounts(r) geneCounts(r) universeCounts(r) universeMappedCount(r) geneMappedCount(r) geneIds(r) geneIdUniverse(r) condGeneIdUniverse(r) geneIdsByCategory(r, catids = NULL) sigCategories(r, p) ## R CMD check doesn't like these ## annotation(r) ## description(r) testName(r) pvalueCutoff(r) testDirection(r) chrGraph(r)
r |
An instance of a subclass of
HyperGResultBase . |
catids |
A character vector of category identifiers. |
p |
Numeric p-value used as a cutoff for selecting a subset of the result. |
"integer"
vector: for each category term tested, the number of genes from
the gene set that are annotated at the term."numeric"
vector: the ordered p-values for each category term tested."integer"
vector: for each category term tested, the number of genes from
the gene universe that are annotated at the term."integer"
vector of length one giving the size of the gene universe set."numeric"
vector
giving the expected number of genes in the selected gene list to
be found at each tested category term."numeric"
vector giving
the odds ratio for each category term tested.geneIdUniverse
, but each vector of gene IDs is
intersected with the list of selected gene IDs from
geneIds
. The result is the selected gene IDs annotated at
each category.p
is
missing, then the cutoff obtained from pvalueCutoff(r)
will
be used.length(geneIds(obj))
.pvalueCutoff
slot.testDirection
slot. Contains a string indicating
whether the test was for "over"
or "under"
representation of the categories.TRUE
if the
result was obtained using a conditional algorithm.data.frame
summarizing the test result. Optional
arguments pvalue
and categorySize
allow
specification of maximum p-value and minimum cateogyrSize,
respectively.summary
method. The path of a file to write the
report to can be specified using the file
argument.
The default is file=""
which will cause the report to
be printed to the screen. If you wish to create a single
report comprising multiple results you can set
append=TRUE
. The default is FALSE
(overwrite
pre-existing report file). You can specify a string to use
as an identifier for each table by providing a value for the
label
argument. Additional named arguments will be
passed to the summary
method.
Seth Falcon
hyperGTest
HyperGResult-class
HyperGParams-class
GOHyperGParams-class
KEGGHyperGParams-class