Statomica (version 1.0)

Statomica-package: Statomica utility package

Description

Statomica is a suite of basic functions and classes that are needed for certain packages. It includes three data class structures; XprnSet, xprnSet and xprnSetPair, and functions to create them from basic data matrices and to manage them. XprnSet, xprnSet and xprnSetPair are wrappers of the data class ExpressionSet in Bioconductors R package Biobase.

Details

Package:

Statomica

Type:

Package

Version:

1.0

Date:

2014-09-23

License:

CC BY-NC 4.0

Depends:

R (>= 2.14.0), Biobase, multtest, distr, fBasics, methods

URL:

http://www.r-project.org, http://www.bioconductor.org, http://www.statomics.com

License note:

Creative Commons Attribution-NonCommercial 4.0 International License

available from http://creativecommons.org/licenses/by-nc/4.0

Examples

#check results with: class(z);exprs(z);pData(z);fData(z);annotation(z)

#matrices of intensities:
nfeat <- 4; nsamx <- 8; nsamy <- 6
X <- matrix(runif(nfeat * nsamx, min = 0, max = 100), nfeat, nsamx)
Y <- matrix(runif(nfeat * nsamy, min = 0, max = 200), nfeat, nsamy)

#matrices of log intensities:
x <- log(X)
y <- log(Y)

#data structures: 
pD <- cbind(class.1 = c(rep("brown", 5), rep("white", ncol(x) - 5)),
      class.2 = c(rep("small", 3), rep("big", ncol(x) - 3)))
fD <- data.frame(class.1 = c(rep("lipidA", 2), rep("lipidB", nrow(x) - 2)))

z1 <- nxprnSetPair(x = x, y = y, x.pdata = pD, fdata = "proteins", paired = TRUE, 
      annot = c("A", "B"))
z2 <- nXprnSet(x = Y, fdata = fD, pdata = "healthy", annot = "ratsB")

z3 <- xprnSet(featureData = fD, exprs = x, phenoData = pD, annotation = "ratsA")
z4 <- xprnSetPair(x = xprnSet(expr = y), y = xprnSet(expr = y))
z5 <- xprnSetPair(x = x, y = y)