IntensityData object holding the X and Y intensity data from which the B allele frequency and log R ratio are calculated.
genoData
GenotypeData object.
filename
The name of the genotype GDS or netCDF file to create
file.type
The type of file to create ("gds" or "ncdf")
min.n.genotypes
The minimum number of samples for each genotype at any SNP in order to have non-missing B allele freqency and log R ratio. Setting this parameter to 2 or a similar value is recommended.
call.method
If call.method is 'by.plate', the B allele frequency and log R ratio are calculated for samples delineated by plates. This is the default method. If call.method is 'by.study', the calculation uses all samples at once. If a study does not have plate specifications, 'by.study' is the call.method that must be used.
plate.name
Character string specifying the name of the plate
variable in intenData or genoData. By default, the plate.name is simply 'plate' but oftentimes there are variations, such as 'plateID' or 'plate.num'.
block.size
An integer specifying the number of SNPs to be loaded at one time. The recommended value is around 1000, but should vary depending on computing power.
precision
A character value indicating whether floating point
numbers should be stored as "double" or "single" precision.
compress
The compression level for variables in a GDS file (see
add.gdsn for options.
verbose
Logical value specifying whether to show progress information.
Details
Because this function can take a considerable amount of time and space, sufficient attention should be given to the value used for block.size.
Author(s)
Caitlin McHugh
References
Peiffer D.A., Le J.M., Steemers F.J., Chang W., Jenniges T., and et al. High-resolution genomic profiling of chromosomal aberrations using infinium whole-genome genotyping. Genome Research, 16:1136-1148, 2006.