VanillaICE (version 1.34.0)

CopyNumScanParams-class: 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)
"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