doGlimma: A function to generate MA-plots from Glimma, for all...

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

A function to generate MA-plots from Glimma, for all contrasts.

Description

This function is designed to parse a design and contrasts matrix in order to generate Glimma's interactive MA-plots for all contrasts. The heading for the resulting plot is based on the colnames of the contrasts matrix, so it is important to include the colnames and make them explanatory.

Usage

doGlimma(
  tablst,
  datobj,
  dsgn,
  cont,
  grpvec,
  padj = "BH",
  sigfilt = 0.05,
  extraname = NULL,
  ID = NULL,
  sample.cols = rep("#1f77b4", ncol(datobj)),
  ...
)

Arguments

tablst	An MArrayLM object or list of DGEExact or DGELRT objects
datobj	A DGEList, ExpressionSet, EList or matrix
dsgn	A design matrix
cont	A contrast matrix
grpvec	A vector of groups, usually what was used to make the design matrix
padj	Method for multiplicity adjustment. BH by default
sigfilt	Significance cutoff for selecting genes
extraname	Used to add a sub-directory to the glimma-plots directory, mainly used to disambiguate contrasts with the same name (see below).
ID	Character, default is NULL. The column name of the genes list item (from the MArrayLM, DGEExact or DGELRT objects) that will be used for labeling the individual gene expression plot at the top right of the resulting plot. The default of NULL will search for a column labeled SYMBOL to use. If the ID value doesn't match any column, and there is no SYMBOL column, then the default for glMDPlot will be used.
sample.cols	A vector of numbers or hex strings, the same length as the grpvec. This will cause the samples in the upper right plot to have different colors. Useful primarily to check for batch differences. The default is the default from glMDPlot.
...	Allows end users to pass other arguments to the Glimma glMDPlot function

Details

In addition, if there are multiple contrasts with the same name, say if the same comparisons are being made for different tissue types, the extraname argument will cause the output to be placed in glimma-plots/<extraname>, to eliminate over-writing of existing files.

Value

A character vector of the files generated, useful for using as links to the output.

Author(s)

James W. MacDonald [e-mail]

Examples

  ## Not run: 
    mat <- matrix(rnorm(1e6), ncol = 20)
    grps <- factor(1:4, each=5)
    design <- model.matrix(~0 + grps)
    colnames(design) <- LETTERS[1:4]
    contrast <- matrix(c(1,-1,0,0,1,0,-1,0,1,0,0,-1,0,1,-1,0,0,1,0,-1),
    ncol = 5)
    colnames(contrast) <- paste(LETTERS[c(1,1,1,2,2)],
    LETTERS[c(2,3,4,3,4)], sep = " vs ")
    fit <- lmFit(mat, design)
    fit2 <- contrasts.fit(fit, contrast)
    fit2 <- eBayes(fit2)
    htmllinks <- doGlimma(fit2, mat, design, contrast, grps)
   
## End(Not run)

jmacdon/affycoretools documentation built on Nov. 2, 2024, 1:29 a.m.