Usage
appraise(dtab, discretize = TRUE, reduceToSNP = TRUE, prefix, folder = paste0(prefix, "_APPROUT"), discfmlas_in = GGtools:::.discfmlas.demo,
txlist = list( distcats = function(x) { cut(x$mindist, c(-1, seq(0, 200001, 50000))) }, fdrcats = function(x) { fdrfac = cut(x$fdr, c(-.01, .05, .1, .25, .5, 1.01)) relevel(fdrfac, "(0.5,1.01]") }, mafcats = function(x) { maffac = cut(x$MAF,c(-0.01,.05, .1, .25, .51)) relevel(maffac, "(-0.01,0.05]") }, caddcats = function(x){ cut(x$PHRED, c(-.01, 5, seq(10, 30, 10 ), 60)) } ), cutts = c(-0.01,seq(0.015,.12,.015),.15), names2check= GGtools:::.standardNames, maxit=30, savePinfer=FALSE)
# bindgwava( gwavadt, eqdt )
Arguments
dtab
data.table instance as created by transforming
cisRun to GRanges and then to data.table, and
then adding CADD PHRED scores if available. If CADD
PHRED scores are not available, the default formulas
should not be used.
discretize
logical telling whether binning to factors defined in txlist
should be performed
reduceToSNP
logical telling whether ranges should be reduced to
unique SNP and FDR recomputed
prefix
character atom used to prefix objects saved and folder for
result objects
folder
folder name suffix
discfmlas_in
named list of model formulae
txlist
named list of functions that are used to
bin certain quantitative features of SNP
cutts
numeric vector of thresholds for tabulation and discrete calibration
names2check
if NULL, ignored; if a character vector, function
will fail unless all(names2check %in% names(dtab)
maxit
numeric passed to bigglm as control parameter for maximum
number of iterations to use in modeling gwas hit probabilities
savePinfer
logical specifying whether the
inferred probabilities of GWAS involvement are retained