vennSelect {affycoretools} | R Documentation |
This function is designed to output text and/or HTML tables based on
the results of a call to decideTests
.
vennSelect(eset, design, x, contrast, fit, method = "same", adj.meth = "BH", stat = "fstat", otherstats = c("pval","FC"), order.by = "pval", foldFilt = NULL, save = FALSE, ...)
eset |
A ExpressionSet object. |
design |
A design matrix, usually from a call to
model.matrix . See details for more information. |
x |
A TestResults object, usually from a
call to decideTests . |
contrast |
A contrasts matrix, produced either by hand, or by a
call to makeContrasts |
fit |
An MArrayLM object, from a call to
eBayes . |
method |
One of "same", "both", "up", "down", "sameup", or "samedown". See details for more information. |
adj.meth |
Method to use for adjusting p-values. Default is 'BH',
which corresponds to 'fdr'. Ideally one would set this value to be
the same as was used for decideTests . |
stat |
The statistic to report in the resulting HTML
tables. Choices are 'fstat', 'tstat', and NULL . Ideally, the
statistic chosen would correspond to the method used in
decideTests . In other words, if one used
methods such as 'separate' or 'hierarchical', which are based on a
t-statistic, one should choose 'tstat', however, if one used
'nestedF', the logical choice would be 'fstat'. |
otherstats |
Other statistics to be included in the HTML tables. Choices include 'pval' and 'FC'. |
order.by |
Which statistic should be used to order the probesets? Choices include 'fstat', 'tstat', 'pval', and 'FC'. Note that if 'FC' is chosen and there are more than one set of fold changes, the first will be used. |
foldFilt |
A fold change to use for filtering. Default is NULL ,
meaning no filtering will be done. |
save |
Boolean - If TRUE , output a count of genes that
fulfill the criteria. Useful for e.g., Sweave-type reports. |
... |
Used to pass other arguments to probes2table , in
particular, to change the argument to anncols
which controls the columns of hyperlinks to online databases (e.g.,
Entrez Gene, etc.). See aaf.handler for more information. |
The purpose of this function is to output HTML and text tables with
lists of genes that fulfill the criteria of a call to
decideTests
as well as the direction of
differential expression.
Some important things to note: First, the names of the HTML and text
tables are extracted from the colnames
of the
TestResults
object, which come from the contrasts matrix, so
it is important to use something descriptive. Second, the method
argument is analogous to the include
argument from
vennCounts
or
vennDiagram
. Choosing "both" will select genes
that are differentially expressed in one or more comparisons,
regardless of direction. Choosing "up" or "down" will select genes
that are only differentially expressed in one direction. Choosing
"same" will select genes that are differentially expressed in the same
direction. Choosing "sameup" or "samedown" will select genes that are
differentially expressed in the same direction as well as 'up' or
'down'.
Note that this is different than sequentially choosing "up" and then "down". For instance, a gene that is upregulated in one comparison and downregulated in another comparison will be listed in the intersection of those two comparisons if "both" is chosen, it will be listed in only one comparison for both the "up" and "down" methods, and it will be listed in the union (e.g., not selected) if "same" is chosen.
Calling the function normally will result in the output of HTML and text tables:
vennSelect(eset, fit, design, x)
Calling the function with save set to TRUE
will output both
HTML and text tables as well as a vector of counts for each
comparison. This is useful when using the function programmatically
(e.g., when making reports using Sweave).
out <- vennSelect(eset, fit, design, x, save = TRUE)
An alternative would be to use vennCounts2
and
vennDiagram
to output a Venn diagram, which is
probably more reasonable since the tables being output are supposed to
be based on a Venn diagram.
Normally called only for the side effect of producing HTML and text
tables. However, setting save to TRUE
will output a vector of
counts that can be used for making Sweave-style reports.
James W. MacDonald <jmacdon@med.umich.edu>