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