reb (version 1.50.0)

cset2band: cset2band

Description

This function will summarize gene expression data by cytogenetic band

Usage

cset2band(exprs, genome, chr = "ALL", organism = NULL, FUN = isAbnormal, ...)

Arguments

exprs

matrix of gene expression data or similar. The rownames must contain the gene identifiers

genome

an associated chromLoc annotation object

chr

a character vector specifying the chromosomes to analyze

organism

character, "h" for human, "m" for mouse, and "r" for rat.; defaults to NULL - loads from chromLocation object

FUN

function by which to aggregate/summarize each cytogenetic band

...

extra arguments passed on to the aggregate/summary function

Value

a matrix with rows representing cytogenetic bands, and columns representing individual samples.

Details

This function loops through each band for a given organism and summarizes the data for genes that lie within each cytogenetic band based upon the input function. For example, a matrix of gene expression values could be used and the mean expression of each band be determined by passing the mean function. Alternative, DNA copy number gains or losses could be predicted using the reb function and regions of likely gain or losses be summarized by cytogenetic band using the isAbnormal function.

Examples

   data(mcr.eset)
   data(idiogramExample)

## Create a vector with the index of normal samples
   norms <- grep("MNC",colnames(mcr.eset@exprs))

## Smooth the data using the default 'movbin' method,
## with the normal samples as reference and median centering
   cset <- reb(mcr.eset@exprs,vai.chr,ref=norms,center=TRUE)

## Mask the result to remove noise
   exprs <- cset[,-norms]
   exprs[abs(exprs) < 1.96] <- NA

## Starting data
   midiogram(exprs,vai.chr,method="i",col=.rwb,dlim=c(-4,4))

## Summarize each cytogenetic band
   banded <- cset2band(exprs,vai.chr,FUN=mean,na.rm=TRUE)

## Create chromLocation object based on human cytobands
   h.cyto <- buildChromCytoband(organism = "h")

## Plot all data using mideogram
   midiogram(banded,h.cyto,method="i",col=.rwb,dlim=c(-4,4))