byGeneTable: Converting a Segmentation Table Into a By-Gene Table
In rCGH: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data

Description Usage Arguments Details Value Author(s) See Also Examples

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.

1 2	byGeneTable(segTable, symbol = NULL, genome = c("hg19", "hg18", "hg38"), columns = NA, verbose = TRUE)

`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.

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

An object of class "rCGH"

Frederic Commo

getSegTable

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