byGeneTable: Converting a Segmentation Table Into a By-Gene Table

Description

This function creates a by-gene table by listing all the genes contained in each of the segments in the segmentation table. Gene annotations (symbol, location,...), segmented Log2Ratios, and segment legnth are reported in the final table. A supplementary score is the relativeLog: the magnitude, in Log2, from the closest centromere.

Usage

byGeneTable(segTable, symbol = NULL,
        genome = c("hg19", "hg18", "hg38"), columns = NA, verbose = TRUE)

Arguments

segTable

: data frame. A segmentation table exported from an object of class "rCGH"

symbol

: character. A valid HUGO symbol. When NULL the full gene table is returned, the corresponding gene information only o/w.

genome

: string. The genome build to use. Supported genomes are hg18, hg19 (default), and hg38.

columns

: string. what supplementary genes annotations to export. Allowed annotations are those supported by the select method from the AnnotationDbi bioconductor package. When NA (default), 'SYMBOL','ENTREZID', 'GENENAME' and 'MAP' are exported.

verbose

: logical. When TRUE progress is printed.

Value

An object of class "rCGH"

Details

For gene annotations, Hg19/GRCh37 annotations downloaded from NCBI are considered.

Examples

Run this code

filePath <- system.file("extdata", "Affy_cytoScan.cyhd.CN5.CNCHP.txt.bz2",
    package = "rCGH")
cgh <- readAffyCytoScan(filePath, sampleName = "AffyScHD")
cgh <- adjustSignal(cgh, nCores=1)
cgh <- EMnormalize(cgh)
cgh <- segmentCGH(cgh, nCores=1)
st <- getSegTable(cgh)
bygene <- byGeneTable(st)
head(bygene)