computeStat {bsseq} | R Documentation |
Compute a test statistic based on smoothed whole-genome bisulfite sequencing data.
computeStat(BSseqStat, coef = NULL)
BSseqStat |
An object of class |
coef |
A vector indicating for which coefficients the statistic is to
be computed ( |
TODO
An object of class BSseqStat. More speciically, the input
BSseqStat object with the computed statistics added to the
stats
slot (accessible with getStats
).
Kasper Daniel Hansen khansen@jhsph.edu
smoothSds
for the function to create the appropriate
BSseqStat
input object.
BSseqStat
also describes the return class. This
function is likely to be followed by the use of dmrFinder
.
if(require(bsseqData)) { data(keepLoci.ex) data(BS.cancer.ex.fit) BS.cancer.ex.fit <- updateObject(BS.cancer.ex.fit) ## Remember to subset the BSseq object, see vignette for explanation ## TODO: Kind of a forced example design <- model.matrix(~0 + BS.cancer.ex.fit$Type) colnames(design) <- gsub("BS\\.cancer\\.ex\\.fit\\$Type", "", colnames(design)) contrasts <- makeContrasts( cancer_vs_normal = cancer - normal, levels = design ) BS.stat <- BSmooth.fstat(BS.cancer.ex.fit[keepLoci.ex,], design, contrasts) BS.stat <- smoothSds(BS.stat) BS.stat <- computeStat(BS.stat) BS.stat }