CopyNumScanParams-class {VanillaICE} | R Documentation

## Parameters for parsing source files containing SNP-array processed data, such as GenomeStudio files for the Illumina platform

### Description

Raw SNP array processed files have headers and variable labels that may depend the software, how the output files was saved, the software version, and other factors. The purpose of this container is to collect the parameters relevant for reading in the source files for a particular project in a single container. This may require some experimentation as the example illustrates. The function `fread` in the `data.table` package greatly simplifies this process.

### Usage

    CopyNumScanParams(
      cnvar = "Log R Ratio",
      bafvar = "B Allele Freq",
      gtvar = c("Allele1 - AB", "Allele2 - AB"),
      index_genome = integer(),
      select = integer(),
      scale = 1000,
      row.names = 1L
    )

    ## S4 method for signature 'CopyNumScanParams'
    show(object)

### Arguments

`cnvar` | length-one character vector providing name of variable for log R ratios
`bafvar` | length-one character vector providing name of variable for B allele frequencies
`gtvar` | length-one character vector providing name of variable for genotype calls
`index_genome` | integer vector indicating which rows of the of the source files (e.g., GenomeStudio) to keep. By matching on a sorted GRanges object containing the feature annotation (see example), the information on the markers will also be sorted.
`select` | integer vector specifying indicating which columns of the source files to import (see examples)
`scale` | length-one numeric vector for rescaling the raw data and coercing to class integer. By default, the low-level data will be scaled and saved on disk as integers.
`row.names` | length-one numeric vector indicating which column the SNP names are in
`object` | a `CopyNumScanParams` object

### Slots

`index_genome`

  an integer vector

`cnvar`

  the column label for the log R ratios

`bafvar`

  the column label for the B allele frequencies

`gtvar`

  the column label(s) for the genotypes

`scale`

  length-one numeric vector indicating how the low-level data should be scaled prior to saving on disk

`select`

  numeric vector indicating which columns to read

`row.names`

  length-one numeric vector indicating which column the SNP names are in

### See Also

`ArrayViews` `parseSourceFile`

### Examples

    CopyNumScanParams() ## empty container

[Package VanillaICE version 1.50.0 Index]