vennSelect: Select and Output Genelists Based on Venn Diagrams

Description

This function is designed to output text and/or HTML tables based on the results of a call to decideTests.

Usage

vennSelect(eset, design, x, contrast, fit, method = "same", adj.meth = "BH", stat = "fstat", otherstats = c("pval", "FC"), order.by = "pval", foldFilt = NULL, save = FALSE, titleadd = NULL, ...)

Arguments

eset

An ExpressionSet object.

design

A design matrix.

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 log fold change to filter results.

save

Boolean. Save the results for further processing?

titleadd

Additional text to add to the title of the HTML tables. Default is NULL, in which case the title of the table will be the same as the filename.

...

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.

Value

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.

Details

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.