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NAMESPACE
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NAMESPACE
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export(
snp,
setupSNP,
plotMissing,
tableHWE,
WGstats,
WGassociation,
scanWGassociation,
getSignificantSNPs,
Bonferroni.sig,
association,
additive,
codominant,
dominant,
overdominant,
odds,
recessive,
pvalues,
intervals,
int,
interactionPval,
make.geno,
haplo.interaction,
permTest,
qqpval,
GenomicControl,
maxstat,
LD,
LDplot,
LDtable,
getNiceTable,
getGeneSymbol,
Table.N.Per,
Table.mean.se,
is.Monomorphic,
sortSNPs,
related
)
import("haplo.stats")
import("survival")
import("mvtnorm")
import("ggplot2")
importFrom("tidyr", "gather")
importFrom("poisbinom", "dpoisbinom" )
importFrom("parallel", "mclapply")
importFrom("plyr", "arrange", "count")
importFrom("grDevices", "heat.colors")
# importFrom("Biostrings", "getSeq", "DNA_BASES")
importFrom("graphics", "abline", "axis", "barplot", "hist", "image",
"layout", "legend", "lines", "matplot", "par", "segments",
"strheight", "strwidth", "text", "title")
importFrom("stats", ".getXlevels", "AIC", "anova", "as.formula",
"binomial", "complete.cases", "dbeta", "density",
"fisher.test", "gaussian", "glm", "glm.control", "glm.fit",
"is.empty.model", "median", "model.extract", "model.matrix",
"model.offset", "model.response", "model.weights",
"na.omit", "nlm", "optimize", "pchisq", "pnorm",
"printCoefmat", "qbeta", "qchisq", "qnorm", "relevel",
"runif", "sd", "terms", "reorder")
S3method(summary,haplo.glm)
S3method(intervals,haplo.glm)
S3method(intervals,dif)
S3method(intervals,or)
S3method(print,haploOut)
S3method(print,intervals)
S3method(print,snpOut)
S3method(print,tableHWE)
S3method(codominant,default)
S3method(dominant,default)
S3method(recessive,default)
S3method(overdominant,default)
S3method(additive,default)
S3method(codominant,snp)
S3method(dominant,snp)
S3method(recessive,snp)
S3method(overdominant,snp)
S3method(additive,snp)
S3method(plot,snp)
S3method(reorder,snp)
S3method(summary,snp)
S3method(print,snp)
S3method("[",snp)
S3method(print,summary.snp)
S3method(plot,SNPinteraction)
S3method(print,SNPinteraction)
S3method(summary,setupSNP)
S3method("[",setupSNP)
S3method("[[<-",setupSNP)
S3method("[<-",setupSNP)
S3method("$<-",setupSNP)
S3method(labels,setupSNP)
S3method(plot,setupSNP)
S3method(summary,WGassociation)
S3method(print,WGassociation)
S3method(plot,WGassociation)
S3method(pvalues,WGassociation)
S3method(codominant,WGassociation)
S3method(dominant,WGassociation)
S3method(recessive,WGassociation)
S3method(overdominant,WGassociation)
S3method(additive,WGassociation)
S3method("[",WGassociation)
S3method(c,WGassociation)
S3method(labels,WGassociation)
S3method(print,permTest)
S3method(plot,permTest)
S3method(print,maxstat)
S3method(maxstat,default)
S3method(maxstat,table)
S3method(maxstat,setupSNP)
S3method(maxstat,matrix)
S3method(LD,snp)
S3method(LD,setupSNP)
S3method(print,LD)
S3method(print,LD.data.frame)
S3method(summary,LD.data.frame)
S3method(print,summary.LD.data.frame)
##################
# hidden functions
# as.snp
# is.quantitative
# is.snp
# association.fit
# crea.lab
# expandsetupSNP
# extractPval
# extractPval.i
# GenotypeRate
# haplo.inter.fit
# orderChromosome
# SNPHWE
#
# table.corner
# table.interaction
# togeno
# Table.N.Per
# Table.mean.se
# pvalTest
# modelTest
# assoc