openSesame {sesame} | R Documentation |
This function is a simple wrapper of noob + nonlinear dye bias correction + pOOBAH masking.
openSesame(x, platform = "", manifest = NULL, BPPARAM = SerialParam(), ...)
x |
SigDF(s), IDAT prefix(es), minfi GenomicRatioSet(s), or RGChannelSet(s) |
platform |
optional platform string |
manifest |
optional dynamic manifest |
BPPARAM |
get parallel with MulticoreParam(n) |
... |
parameters to getBetas |
If the input is an IDAT prefix or a SigDF
, the output is
the beta value numerics. If the input is a minfi GenomicRatioSet
or RGChannelSet, the output is the sesamized GenomicRatioSet.
a numeric vector for processed beta values
sdf <- sesameDataGet('HM450.1.TCGA.PAAD')$sdf IDATprefixes <- searchIDATprefixes( system.file("extdata", "", package = "sesameData")) betas <- openSesame(IDATprefixes)