bgx (version 1.38.0)

analysis.bgx: Analyse BGX output.

Description

Functions for plotting expression densities, differential expression densities, histogram of proportion of differentially expressed genes, etc.

Usage

plotExpressionDensity(bgxOutput, gene=NULL, normalize=c("none","mean","loess"),...) plotDEDensity(bgxOutput, gene=NULL, conditions=c(1,2), normalize=c("none","mean","loess"), normgenes=c(1:length(bgxOutput[["geneNames"]])), ...) plotDEHistogram(bgxOutput, conditions=c(1,2), normalize=c("none","mean","loess"), normgenes=c(1:length(bgxOutput[["geneNames"]])), df=floor(1.8 * log10(length(bgxOutput[["geneNames"]])))) rankByDE(bgxOutput, conditions=c(1,2),normalize=c("none", "mean", "loess"), normgenes=c(1:length(bgxOutput[["geneNames"]])), absolute=TRUE) plotDiffRank(bgxOutput, conditions=c(1,2),normalize=c("none", "mean", "loess"), normgenes=c(1:length(bgxOutput[["geneNames"]])), ymax=NULL)

Arguments

bgxOutput

A list obtained from running readOutput.bgx on a BGX output directory.

gene

Which gene to analyse. This can either be an index or a name.

conditions

Indices of conditions to compare.

normalize

"none": do not normalise posterior distributions of mu. "mean": normalise by scaling posterior distributions of mu for conditions > 1 to have the same mean as the posterior distribution of mu for condition 1. "loess": same as "mean" but use loess normalisation.

normgenes

Which genes to use for loess normalisation. By default, use all genes.

df

Residual degrees of freedom. Decrease to 6 if the histogram fit goes haywire.

absolute

Rank genes by absolute differential expression.

ymax

Specify upper limit of y axis.

...

Parameters to pass to density function (where applicable).

Value

None, except plotDERank, which returns a matrix of genes ranked by differential expression.

Details

plotExpressionDensity plots gene expression distributions under various conditions for the specified gene.

plotDEDensity plots the differential expression distribution between two conditions for a given gene.

plotDEHistogram plots a histogram of differential expression between two conditions and estimates the number of up and down regulated differentially expressed genes.

rankByDE ranks genes by differential expression and returns ordering and corresponding DE values in a matrix.

plotDiffRank plots 2.5-97.5% confidence intervals for ranked differential expression estimates.

See Also

bgx, standalone.bgx, readOutput.bgx, plotExpressionDensity, plotDEDensity, plotDEHistogram