PSigA: PsigA: A gene-signature ranking method based on sample...

In sidiropoulos/PSigA: A gene-signature ranking method based on sample density in PCA space

Description

The PsigA package provides a set of functions to perform Principal Component analysis based on genetic pathways. Moreover PSigA incorporates an algorithm to measure the spread of the data in the PCA space and rank the gene-signatures based on their ability to split the data in distinct entities.

PsigA blah blah

Usage

PsigA(data, signatures, threshold = 0.005, n = 200, magnitude = FALSE,
  scale = FALSE, report = TRUE, p.adj = p.adjust.methods,
  min.length = 10, max.length = 500)

Arguments

data	data frame of matrix with gene expression values where rows represent genes and columns represent samples.
signatures	list where every entry is a character vector of the gene names that correspond to a gene-pathway. If the gene format is different from the one in rownames(data), use parseData first.
threshold	low density cutoff. Used in peakDistance2d.
n	Number of grid points in each direction. Can be scalar or a length-2 integer vector. See kde2d.
magnitude	When TRUE the score is multiplied by the cluster density. Default: FALSE.
scale	a logical value indicating whether the variables should be scaled to have unit variance before the analysis takes place. See prcomp for more details.

Value

A data frame with 2 columns; 1) score, the PsigA score of a given signature and 2) size, the number of genes in the signature that were found in the data. If parsed = FALSE, the function returns a list, where the first entry contains the data frame described above and the second entry the parsed data.

Examples

require(Biobase)
require(breastCancerVDX)
data(vdx)
data(RAPIN)

VDX <- parseData(data = exprs(vdx), geneIds = fData(vdx)$Gene.symbol)

scores <- PsigA(VDX, RAPIN, threshold = 0.003)
head(scores)

#plot top signature
sigPlot(VDX, RAPIN[[rownames(scores)[1]]])
sigBiplot(VDX, RAPIN[[rownames(scores)[1]]], factor(pData(vdx)$grade),
          main = rownames(scores)[1])

sidiropoulos/PSigA documentation built on May 29, 2019, 9:58 p.m.