outputRomer: A function to create HTML output from the results of running...

In affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Description

This function is actually intended to be a sub-function of runRomer, but can hypothetically run by itself if the romer step has already been done.

Usage

outputRomer(object, fit, ...)

## S4 method for signature 'ExpressionSet,MArrayLM'
outputRomer(
  object,
  fit,
  rsltlst,
  genesetlst,
  design = NULL,
  contrast = NULL,
  changenames = TRUE,
  dir = "genesets",
  explanation = NULL,
  baseline.hmap = TRUE,
  file = "indexRomer.html",
  affy = TRUE,
  ...
)

## S4 method for signature 'DGEList,DGEGLM'
outputRomer(
  object,
  fit,
  rsltlst,
  genesetlst,
  design = NULL,
  contrast = NULL,
  changenames = TRUE,
  dir = "genesets",
  explanation = NULL,
  baseline.hmap = TRUE,
  file = "indexRomer.html",
  ...
)

## S4 method for signature 'EList,MArrayLM'
outputRomer(
  object,
  fit,
  rsltlst,
  genesetlst,
  design = NULL,
  contrast = NULL,
  changenames = TRUE,
  dir = "genesets",
  explanation = NULL,
  baseline.hmap = TRUE,
  file = "indexRomer.html",
  ...
)

Arguments

object	An ExpressionSet, DGEList or EList object containing normalized, summarized gene expression data.
fit	An MArrayLM or DGEGLM object, containing the fitted data.
...	Arguments to be passed to lower-level functions. See geneSetPage, dataAndHeatmapPage and gsHeatmap for available arguments.
rsltlst	A list of results, generated by the romer function. See discussion for more information.
genesetlst	A list of genesets, usually created by loading in the RData files that can be downloaded from http://bioinf.wehi.edu.au/software/MSigDB/. See details for more information.
design	A design matrix describing the model.
contrast	A contrast matrix describing the contrasts that were fit. This matrix should have colnames, which will be used to name subdirectories containing results.
changenames	Boolean. When creating heatmaps of the gene sets, should the columns be appended with the colnames from the design matrix? If FALSE, the sampleNames will be used.
dir	Character. The subdirectory to use for the output data. Defaults to 'genesets'.
explanation	If NULL, a generic paragraph will be placed at the top of the indexRomer.html page, giving a brief explanation of the analysis. Alternatively, this can be replaced with other text. Please note that this text should conform to HTML standards (e.g., will be pasted into the HTML document as-is, so should contain any required HTML markup).
baseline.hmap	Boolean. If TRUE, then the resulting heatmaps will be centered by subtracting the mean of the baseline sample. As an example, in a contrast of treatment A - treatment B, the mean of the treatment B samples will be subtracted. The heatmap colors then represent the fold change between the A and B samples.
file	Character. The filename to output. Defaults to indexRomer.html.
affy	Boolean. Are these Affymetrix arrays? if TRUE, then thre will be links generated in the HTML table to the netaffx site.

Details

This function is intended to be an internal function for runRomer. However, it is possible that runRomer errored out after saving the results from running romer on a set of contrasts, and all that remains is to create the output HTML.

Please note that the first two arguments to this function have certain expectations. The rsltlst should be the output from running romer. If using the saved output from runRomer, one should first load the 'romer.Rdata' file, which will introduce a list object with the name 'romerlst' into the working directory, so the first argument should be rsltlst = romerlst.

Second, see the code for runRomer, specifically the line that creates the 'sets' object, which will show how to create the correct genesetlst object.

Value

Nothing is returned. The function is run only for the side effect of creating HTML tables with output for each significant gene set.

Methods (by class)

• object = ExpressionSet,fit = MArrayLM: Output romer results using microarray data

• object = DGEList,fit = DGEGLM: Output romer results using RNA-Seq data processed using edgeR

• object = EList,fit = MArrayLM: Output romer results using RNA-Seq data processed using voom.

Author(s)

James W. MacDonald <[e-mail]>

affycoretools documentation built on Nov. 8, 2020, 6 p.m.