vennSelectFC {affycoretools} | R Documentation |
This function is designed to output text and/or HTML tables based on
the results of a call to foldFilt
. The general idea being that
one might want to create a Venn diagram showing probesets that are
unique to particular comparisons, or consistent between comparisons,
and then might want to output the probesets that are contained in each
cell of the Venn diagram.
vennSelectFC(eset, x, comps, order.by = "sum", method = "same", text = TRUE, html = TRUE, ...)
eset |
A ExpressionSet object. |
x |
An indicator matrix showing up or down regulation based on
fold change, usually from a call to foldFilt . See details for
more information. |
comps |
A list containing all the comparisons to be
made. Each list item should be a vector of length two. This should
be identical to the 'comps' argument used in the call to
foldFilt See details for more information. |
order.by |
One of 'sum', 'max', 'median', or 'mean'. This orders the output for those tables that have multiple fold change values based on the summary statistic chosen. Defaults to 'sum'. |
method |
One of "same", "both", "up", "down", "sameup", or "samedown". See details for more information. |
text |
Boolean. Output text tables? Defaults to TRUE |
html |
Boolean. Output HTML tables? Defaults to TRUE |
... |
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 the probesets listed in a
Venn diagram that has been produced by a call to foldFilt
. A
small example would be as follows:
Assume an ExpressionSet
exists that contains expression values
for three Affymetrix chips, say a control, and two experimentals. One
might want to know what probesets are different between each of the
experimentals and the control, and those that are different between
both of the experimentals and the control. We first make the
comparisons, based on a fold change of 2 (or a difference of 1 on the
log scale).
comps <- list(c(1,2), c(1,3))
This list indicates what comparisons we want. In this case 1vs2 and 1vs3.
out <- foldFilt(eset, fold = 1, groups = 1:3, comps = comps, compnames=c("Control vs experimental1", "Control vs experimental2"), save = TRUE)
By setting save = TRUE, we are saving a list, the first item being a
vector of the number of probesets in each comparison, the second item
being an indicator matrix showing up or down regulation based on a
two-fold difference. We could make a Venn diagram using this matrix
with vennCounts2
and vennDiagram
. If we
then wanted to output the probesets in each cell of that Venn diagram,
we could use vennSelectFC
as follows:
vennSelectFC(eset, out[[2]], comps)
One thing to note here is that the names of the resulting tables as
well as the columns containing the fold change values will be
extracted from the column names of the indicator matrix. This matrix
will get its column names from the 'compnames' argument to
foldFilt
, so it is best to use reasonable names here. Also note
that any character used in the 'compnames' argument that is not a
valid character for a file name will be stripped out.
Called only for the side effect of outputting HTML and/or text tables.
James W. MacDonald <jmacdon@med.umich.edu>