NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(as.data.frame,MiDAS)
export(HWETest)
export(analyzeAssociations)
export(analyzeConditionalAssociations)
export(checkAlleleFormat)
export(checkKirGenesFormat)
export(convertAlleleToVariable)
export(countsToVariables)
export(filterByFrequency)
export(filterByOmnibusGroups)
export(filterByVariables)
export(getAAFrequencies)
export(getAlleleResolution)
export(getAllelesForAA)
export(getExperiments)
export(getFrequencies)
export(getHlaCalls)
export(getHlaFrequencies)
export(getHlaKirInteractions)
export(getKIRFrequencies)
export(getKirCalls)
export(getOmnibusGroups)
export(getPlaceholder)
export(getVariableAAPos)
export(hlaCallsGranthamDistance)
export(hlaToAAVariation)
export(hlaToVariable)
export(kableResults)
export(omnibusTest)
export(prepareMiDAS)
export(readHlaAlignments)
export(readHlaCalls)
export(readKirCalls)
export(reduceAlleleResolution)
export(reduceHlaCalls)
export(runMiDAS)
export(summariseAAPosition)
exportClasses(MiDAS)
exportMethods(filterByFrequency)
exportMethods(filterByOmnibusGroups)
exportMethods(filterByVariables)
exportMethods(getAllelesForAA)
exportMethods(getExperiments)
exportMethods(getFrequencies)
exportMethods(getHlaCalls)
exportMethods(getKirCalls)
exportMethods(getOmnibusGroups)
exportMethods(getPlaceholder)
importClassesFrom(MultiAssayExperiment,MultiAssayExperiment)
importFrom(HardyWeinberg,HWChisqStats)
importFrom(MultiAssayExperiment,ExperimentList)
importFrom(MultiAssayExperiment,MultiAssayExperiment)
importFrom(MultiAssayExperiment,colData)
importFrom(MultiAssayExperiment,experiments)
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assay)
importFrom(assertthat,assert_that)
importFrom(assertthat,is.count)
importFrom(assertthat,is.flag)
importFrom(assertthat,is.number)
importFrom(assertthat,is.readable)
importFrom(assertthat,is.string)
importFrom(assertthat,noNA)
importFrom(assertthat,see_if)
importFrom(broom,tidy)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,ends_with)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_at)
importFrom(dplyr,n)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,starts_with)
importFrom(dplyr,summarise)
importFrom(dplyr,tibble)
importFrom(dplyr,vars)
importFrom(formattable,percent)
importFrom(kableExtra,add_header_above)
importFrom(kableExtra,kable_styling)
importFrom(kableExtra,scroll_box)
importFrom(knitr,kable)
importFrom(magrittr,"%<>%")
importFrom(magrittr,"%>%")
importFrom(methods,is)
importFrom(methods,new)
importFrom(methods,setClass)
importFrom(methods,validObject)
importFrom(qdapTools,mtabulate)
importFrom(rlang,"!!")
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,abort)
importFrom(rlang,call_modify)
importFrom(rlang,has_name)
importFrom(rlang,is_empty)
importFrom(rlang,is_formula)
importFrom(rlang,is_integerish)
importFrom(rlang,list2)
importFrom(rlang,parse_expr)
importFrom(rlang,parse_exprs)
importFrom(rlang,warn)
importFrom(stats,formula)
importFrom(stats,getCall)
importFrom(stats,logLik)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pchisq)
importFrom(stats,reshape)
importFrom(stats,resid)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(stats,update)
importFrom(stringi,stri_count_fixed)
importFrom(stringi,stri_detect_regex)
importFrom(stringi,stri_flatten)
importFrom(stringi,stri_read_lines)
importFrom(stringi,stri_split_fixed)
importFrom(stringi,stri_split_regex)
importFrom(stringi,stri_sub)
importFrom(stringi,stri_subset_fixed)
importFrom(tibble,rownames_to_column)
importFrom(utils,methods)
importFrom(utils,read.table)
importFrom(utils,type.convert)