chromosomesPosition {CNAnorm} | R Documentation

## Accessors methods for Function ratio in Package ‘CNAnorm’

### Description

`chrs` returns/set the name of chromosomes/contigs

`arms` retruns the name of the chromosome and arm. A data frame containing ideogram information has to be provided. See ?hg19_hs_ideogr for an example

`pos` returns/set the position of starting window. Be careful! If you need to change data, it is better to change the input data and start over.

### Usage

    chrs(object)
    ## S4 method for signature 'CNAnorm'
    pos(object, show = "start")
    ## S4 method for signature 'CNAnorm'
    arms(object, banding_df)

### Arguments

`object` | An object of Class `"CNAnorm"`
`show` | The position to show: 'start', 'end'
`banding_df` | A data frame with infromation about ideogram

### Value

`chrs` and `arms` return a character vector, `pos` returns a numeric vector

### Author(s)

Stefano Berri <s.berri@leeds.ac.uk>

### See Also

`gcNorm`, `CNAnorm-class`, `hg19_hs_ideogr`

### Examples

    data(LS041)
    data(hg19_hs_ideogr)
    CN <- dataFrame2object(LS041)
    dataFrameNames <- as.character(LS041$Chr)
    objectNames <- chrs(CN)
    armNames <- arms(CN, hg19_hs_ideogr)
    # check the names are, indeed, the same
    all(dataFrameNames == objectNames)
    # make shorter names, drop the first three letters ('chr')
    shortNames <- substr(chrs(CN),4,nchar(chrs(CN)))
    chrs(CN) <- shortNames

    # retrieve all new names
    unique(chrs(CN))
    unique(armNames)

[Package CNAnorm version 1.38.0 Index]