RBM-package: RBM:a package for microarray and RNA-Seq data analysis

In RBM: RBM: a R package for microarray and RNA-Seq data analysis

Description

Use A Resampling-Based Empirical Bayes Approach to Assesse Differential Expression or Identifying differntially methylated loci in Two-Color Microarrays and RNA-Seq data sets. Significant features selected through RBM_T or RBM_F functions could be further used as input for pathway analysis or experimental vilidations.

Details

Package:	RBM
Type:	Package
Version:	0.99.0
Date:	2014-10-05
Depends:	R (>= 3.0.0), limma, marray
License:	GPL (>= 2)

Author(s)

Dongmei Li and Chin-Yuan Liang Maintainer: Dongmei Li <[e-mail]> and Chin-Yuan Liang <[e-mail]>

References

Li D, Le Pape MA, Parikh NI, Chen WX, Dye TD (2013) Assessing Differential Expression in Two-Color Microarrays: A Resampling-Based Empirical Bayes Approach. PLoS ONE 8(11): e80099. doi: 10.1371/journal.pone.0080099

See Also

The RBM_T and RBM_F functions defined in this package. The limma and marray packages.

Examples

normal_data <- matrix(rnorm(200*6), 200, 6)
mydesign <- c(0,0,0,1,1,1)
norm_result <- RBM_T(normal_data,mydesign,50,0.05)
    
unif_data <- matrix(runif(200*7, 0.10, 0.95), 200, 7)
mydesign2 <- c(0,0,0, 1,1,1,1)
unif_result <- RBM_T(unif_data,mydesign2,100,0.05)
    
normdata_F <- matrix(rnorm(200*9, 0, 2), 200, 9)   
mydesign_F <- c(0, 0, 0, 1, 1, 1, 2, 2, 2)
aContrast <- c("X1-X0", "X2-X1", "X2-X0")
normresult_F <- RBM_F(normdata_F, mydesign_F, aContrast, 100, 0.05) 
     
unifdata_F <- matrix(runif(200*18, 0.15, 0.98), 200, 18) 
mydesign2_F <- c(rep(0, 6), rep(1, 6), rep(2, 6))
aContrast <- c("X1-X0", "X2-X1", "X2-X0")
unifresult_F <- RBM_F(unifdata_F, mydesign2_F, aContrast, 100, 0.05) 

Example output

Loading required package: limma
Loading required package: marray

RBM documentation built on Nov. 8, 2020, 8:11 p.m.