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
Details
The appraise function wraps many tasks used to appraise eQTL
collections in terms of predictive capacity. Details
will be provided.
Value
A folder is opened and objects are written
representing the test set (data.table on SNPs on even chromosomes),
the coefficients of predictive models built on training set
(SNPs on odd chromosomes), coefficients of linear regressions
of binary test outcomes for calibrating the model on test data,
and ROC AUC measures.
bindgwava uses simple data.table operations with match to
add three columns to eqdt, gwava_tss, gwava_unmat, and gwava_regi