gene.cn(FASeg)R Documentation

Generates gene-level copy number information

Description

Given fitted copy number data and gene/cytoband information, this function generates a matrix of gene-level copy number and cytoband information.

Usage

gene.cn(fitted, gene.info=gene.h18,band.info=band.h18, compress=FALSE, cnv.cutoff=c(1.5, 2.5))

Arguments

fitted Fitted copy number data.
gene.info A table containing gene location in the genome, see gene.h17.
band.info A table containing cytoband location in the genome, see band.h17.
compress If false, each gene will occupy a row in the resulting matrix. If true, adjacent genes with same copy numbers will be compressed into a single row.
cnv.cutoff copy number values outside these cutoff are considered CNV; the frequencies are reported at the end of each row.

Details

Value

A matrix is returned. The first column is chromosome number; the second is the starting position of the gene; the third is the ending position; the fourth is gene ID; the remaining columns contain copy numbers of the genes in each sample, cytoband the genes belong to, and the frequencies of CNV.

Note

In the compressed table, for merged genes, only the first and the last are shown. Genes in the middle need to be found in the uncompressed table.

Author(s)

Tianwei Yu (tyu8@sph.emory.edu)

References

See Also

Examples

  data(gene.h18)
  data(band.h18)
  data(sample.fitted)
  gene.level<-gene.cn(sample.fitted, gene.h18, band.h18)
[Package FASeg version 2.0 Index]