cset2band: cset2band

In reb: Regional Expression Biases

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

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.

Value

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

Author(s)

Karl Dykema

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))

reb documentation built on April 28, 2020, 8:35 p.m.