hapmapProbabilities {VanillaICE} | R Documentation |
Wrapper for extracting the chip-specific distribution of CRLMM confidence scores for HapMap data where we assume we know the true genotype. Presently only supported for Affymetrix 50k and 250k SNP chips and onnly relevant for fitting the ICE HMM (see reference below).
hapmapProbabilities(x)
x |
Name of chip. Must be 'pd.mapping...' |
Confidence scores in a SnpCallSet
created by crlmm
are
stored in the element "pAcc" in the assay data.
Matrix of confidence scores
RB Scharpf et al. (2007), Department of Biostatistics Working Papers, Working Paper 136
crlmm
,
SnpCallSet-class
,
AssayDataElement