Nothing
CheckCharacterClass <- function (DataSource1) {
returnValue <- FALSE
if (is.character(DataSource1)) {
returnValue <- TRUE
}
return(returnValue)
}
CheckVariableExists <- function (DataSource1) {
returnValue <- FALSE
if (exists(DataSource1)) {
returnValue <- TRUE
}
return(returnValue)
}
CheckDataFrameFormat <- function (DataSource1) {
returnValue <- FALSE
if (is.data.frame(eval(parse(text=DataSource1)))) {
returnValue <- TRUE
}
return(returnValue)
}
CheckDataSourceHeaders <- function (DataSources1, ExpectedColumnNames1) {
returnValueVector <- c()
for (DataSource1 in DataSources1) {
returnValue <- TRUE
DataSource1ColumnNames <- names(eval(parse(text=DataSource1)))
for (ExpectedColumnName in ExpectedColumnNames1) {
if (! ExpectedColumnName %in% DataSource1ColumnNames) {
returnValue <- FALSE
}
}
returnValueVector <- c(returnValueVector, returnValue)
}
return(returnValueVector)
}
CheckDataSourceDirectionColumn <- function (DataSources1) {
returnValue <- TRUE
if (length(eval(parse(text=paste(DataSources1, "$Direction", sep="")))[eval(parse(text=paste(DataSources1, "$Direction", sep=""))) != "+" & eval(parse(text=paste(DataSources1, "$Direction", sep=""))) != "-"]) > 0) {
returnValue <- FALSE
}
return(returnValue)
}
CheckDataSourceMAFIsMAF <- function (DataSources1) {
returnValue <- TRUE
if (TRUE %in% eval(parse(text=paste(DataSources1, "$MAF > .5 ", sep="")))) {
returnValue <- FALSE
}
return(returnValue)
}
CheckDataSourceMAFFixed <- function (DataSources1) {
returnValue <- TRUE
returnVector <- eval(parse(text=paste(DataSources1, "$MAF == 0 | ", DataSources1, "$MAF == 1 ", sep="")))
if (TRUE %in% returnVector) {
returnValue <- FALSE
}
return(returnValue)
}
CheckIndividualDataSources <- function (DataSources, GWASsnps, ExpectedColumnNames, SigmaAlphas, MergedDataSources, ProvidedPriors, UseFlatPrior, PruneMarginalHits, PruneMarginalHits_bpWindow, SNPMarginalUnivariateThreshold, SNPMarginalMultivariateThreshold, NminThreshold, bmassSeedValue, LogFile) {
#Loading and checking data
#~~~~~~
if (is.null(MergedDataSources)) {
LogFile <- rbind(LogFile, paste(format(Sys.time()), " -- beginning DataSources checks.", sep=""))
if (!is.vector(DataSources)) {
stop(Sys.time(), " -- input variable DataSources not in vector format. bmass expects DataSources to be a vector of strings. Please fix and rerun bmass.")
}
LogFile <- rbind(LogFile, paste(format(Sys.time()), " -- DataSources passed vector check.", sep=""))
DataSourcesCheckCharacters <- sapply(DataSources, CheckCharacterClass)
if (FALSE %in% DataSourcesCheckCharacters) {
stop(Sys.time(), " -- the following entries in DataSources were not found as characters. Please fix and rerun bmass: ", paste(DataSources[!DataSourcesCheckCharacters], collapse=" "))
}
LogFile <- rbind(LogFile, paste(format(Sys.time()), " -- DataSources passed string check.", sep=""))
DataSourcesCheckExists <- sapply(DataSources, CheckVariableExists)
if (FALSE %in% DataSourcesCheckExists) {
stop(Sys.time(), " -- the variables associated with the following entries in DataSources were not found to exist. Please fix and rerun bmass: ", paste(DataSources[!DataSourcesCheckExists], collapse=" "))
}
LogFile <- rbind(LogFile, paste(format(Sys.time()), " -- DataSources passed exists check.", sep=""))
DataSourcesCheckDataFrames <- sapply(DataSources, CheckDataFrameFormat)
if (FALSE %in% DataSourcesCheckDataFrames) {
stop(Sys.time(), " -- the following data sources are not formatted as data.frames. Please fix and rerun bmass: ", paste(DataSources[!DataSourcesCheckDataFrames], collapse=" "))
}
LogFile <- rbind(LogFile, paste(format(Sys.time()), " -- DataSources passed data.frame check.", sep=""))
DataSourcesCheckHeaderNames <- CheckDataSourceHeaders(DataSources, ExpectedColumnNames)
if (FALSE %in% DataSourcesCheckHeaderNames) {
stop(Sys.time(), " -- the following data sources do not have all the expected column headers. The expected column headers are \"", paste(ExpectedColumnNames, collapse=" "), "\". Please fix and rerun bmass: ", paste(DataSources[!DataSourcesCheckHeaderNames], collapse=" "))
}
LogFile <- rbind(LogFile, paste(format(Sys.time()), " -- DataSources passed column headers check.", sep=""))
DataSourcesCheckDirectionColumn <- sapply(DataSources, CheckDataSourceDirectionColumn)
if (FALSE %in% DataSourcesCheckDirectionColumn) {
stop(Sys.time(), " -- the following data sources have entries other than + and - in the Direction column. Please fix and rerun bmass: ", paste(DataSources[!DataSourcesCheckDirectionColumn], collapse=" "))
}
LogFile <- rbind(LogFile, paste(format(Sys.time()), " -- DataSources passed Direction column check.", sep=""))
DataSourcesCheckMAFIsMAF <- sapply(DataSources, CheckDataSourceMAFIsMAF)
if (FALSE %in% DataSourcesCheckMAFIsMAF) {
stop(Sys.time(), " -- the following data sources have variants whose MAF entry are > .5; bmass expects the MAF column to only have values <= .5. Please fix and rerun bmass: ", paste(DataSources[!DataSourcesCheckMAFIsMAF], collapse=" "))
}
LogFile <- rbind(LogFile, paste(format(Sys.time()), " -- DataSources passed MAF column check.", sep=""))
DataSourcesCheckMAFFixed <- sapply(DataSources, CheckDataSourceMAFFixed)
if (FALSE %in% DataSourcesCheckMAFFixed) {
stop(Sys.time(), " -- the following data sources have variants whose MAF are == 0 (or == 1); bmass expects only segregating variants (eg not fixed). Please fix and rerun bmass: ", paste(DataSources[!DataSourcesCheckMAFFixed], collapse=" "))
} else {
LogFile <- rbind(LogFile, paste(format(Sys.time()), " -- DataSources passed MAF fixed check.", sep=""))
}
if (!is.null(ProvidedPriors)) {
if (!is.vector(ProvidedPriors)) {
stop(Sys.time(), " -- ProvidedPriors input is not in vector format. Please fix and rerun bmass.")
}
if (!is.numeric(ProvidedPriors)) {
stop(Sys.time(), " -- ProvidedPriors input is returning false for is.numeric(). Please ensure all entries are numeric and then rerun bmass.")
}
if (length(ProvidedPriors) != 3^(length(DataSources)*length(SigmaAlphas))) {
stop(Sys.time(), " -- The number of entries in ProvidedPriors does not equal 3 ^ (the number of datasets passed to DataSources * length(SigmaAlphas)) (ie 3 ^ (", as.character(length(DataSources)), " * ", as.character(length(SigmaAlphas)), ") = ", as.character(3^(length(DataSources)*length(SigmaAlphas))), "). Please fix and rerun bmass.")
}
LogFile <- rbind(LogFile, paste(format(Sys.time()), " -- ProvidedPriors was provided and passed checks.", sep=""))
}
if (!is.numeric(NminThreshold)) {
stop(Sys.time(), " -- input variable NminThreshold is not numeric as needed. Please fix and rerub bmass.")
}
} else {
LogFile <- rbind(LogFile, paste(format(Sys.time()), " -- MergedDataSources file provided, going through data checks.", sep=""))
}
return(LogFile)
}
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