dri.sig_genes {DRI}R Documentation

Determine significant genes for DR-Correlate or DR-SAM analysis

Description

Given a cutoff score corresponding to the desired FDR, the list of significant genes is generated, along with each gene's FDR.

Usage

dri.sig_genes(cutoff, observed, null_dist, gene_id, gene_name, chr, 
nuc, bt = TRUE, method = "drcorrelate")

Arguments

cutoff cutoff score for significance from dri.fdrCutoff
observed vector of observed scores from drcorrelate or drsam
null_dist matrix of null data from drcorrelate.null or drsam.null
gene_id vector of gene IDs
gene_name vector of gene names
chr vector of gene chromosome locations
nuc vector of gene nucleotide positions
bt either TRUE or FALSE indicated whether a 2-tail test was performed
method analysis method used, either "drcorrelate" or "drsam"

Value

Results.SigGenes a list of significant genes, positive and negative, with gene-specific FDRs

Author(s)

Keyan Salari, Robert Tibshirani, and Jonathan R. Pollack

References

Salari, K., Tibshirani, R., and Pollack, J.R. (2009) DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data. http://pollacklab.stanford.edu/

See Also

drcorrelate, drcorrelate.null, drsam, drsam.null, dri.fdrCutoff, dri.sig_genes, dri.heatmap, dri.merge.CNbyRNA, dri.smooth.cghdata, runFusedLasso

Examples

require(impute)
data(mySampleData)
attach(mySampleData)

# DNA data should contain no missing values - pre-smooth beforehand
# Impute missing values for gene expression data
RNA.data <- dri.impute(RNA.data)

# DR-Correlate analysis to find genes with correlated DNA/RNA measurements
obs <- drcorrelate(DNA.data, RNA.data, method="pearson")
# generate null distribution for FDR calculation (10 permutations)
null <- drcorrelate.null(DNA.data, RNA.data, method="pearson", perm=10)
# identify the correlation cutoff corresponding to your desired FDR
n.cutoff <- dri.fdrCutoff(obs, null, targetFDR=0.05, bt=TRUE)
cutoff <- n.cutoff[2]
# retrieve all genes that are significant at the determined cutoff, and
# calculate gene-specific FDRs
Results <- dri.sig_genes(cutoff, obs, null, GeneIDs, GeneNames, Chr, Nuc, 
bt=TRUE, method="drcorrelate") 


[Package DRI version 1.1 Index]