vennSelect2: 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, using the ReportingTools package.

Usage

vennSelect2(fit, contrast, design, groups = NULL, cols = NULL,
  p.value = 0.05, lfc = 0, method = "same", adj.meth = "BH",
  titleadd = NULL, fileadd = NULL, baseUrl = ".",
  reportDirectory = "./venns", affy = TRUE, probecol = "PROBEID", ...)

Arguments

fit

An MArrayLM object, from a call to eBayes.

contrast

A contrasts matrix, produced either by hand, or by a call to makeContrasts

design

A design matrix.

groups

This argument is used when creating a legend for the resulting HTML pages. If NULL, the groups will be generated using the column names of the design matrix.

cols

A numeric vector indicating which columns of the fit, contrast and design matrix to use. If NULL, all columns will be used.

p.value

A p-value to filter the results by.

lfc

A log fold change to filter the results by.

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.

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.

fileadd

Additional text to add to the name of the HTML and CSV tables. Default is NULL.

baseUrl

A character string giving the location of the page in terms of HTML locations. Defaults to "."

reportDirectory

A character string giving the location that the results will be written. Defaults to "./venns"

affy

Boolean; are these Affymetrix arrays, and do you want hyperlinks for each probeset to the Affy website to be generated for the resulting HTML tables?

probecol

If the "affy" argument is TRUE, what is the column header for the Affymetrix probeset IDs? Defaults to "PROBEID", which is the default if the data are annotated using a Bioconductor annotation package.

...

Used to pass arguments to lower level functions.

Value

A list with two items. First, a list of HTMLReport objects from the ReportingTools package, which can be used to create an index page with links to the HTML pages created by this function. See the help page for HTMLReport in ReportingTools as well as the vignettes for more information. The second item is a vennCounts object from limma, which can be used to create a Venn diagram, e.g., in a report if this function is called within a Sweave or knitR pipeline.

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.

Unlike vennSelect, this function automatically creates both HTML and CSV output files.