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#' Locus Wrapper
#'
#' Wrapper for main L function
#' @param nloci Number of loci being analyzed.
#' @param loci Loci being analyzed.
#' @param loci.ColNames The column names of the loci being analyzed.
#' @param genos Genotype table
#' @param grp Case/Control or Phenotype groupings.
#' @param Strict.Bin Logical specify if strict rare cell binning should be used in ChiSq test
#' @param Output Data return carryover from main BIGDAWG function
#' @param Verbose Summary display carryover from main BIGDAWG function
#' @note This function is for internal BIGDAWG use only.
L.wrapper <- function(nloci,loci,loci.ColNames,genos,grp,Strict.Bin,Output,Verbose) {
cat("\n>>>> STARTING LOCUS LEVEL ANALYSIS...\n")
Allele.binned <- list() # Alleles binned during chi-square test
Allele.freq <- list() # Alleles Frequencies
overall.chisq <- list() # Chi-Square Table
ORtable <- list() # Odds Ratio Table
Final_binned <- list() # Contingency Table
for(j in 1:nloci) {
# Get Locus
Locus <- loci[j]
# Run Locus Level Analysis
L.list <- L(loci.ColNames,Locus,genos,grp,Strict.Bin)
# Build Output Lists
Allele.binned[[Locus]] <- L.list[['binned']]
Allele.freq[[Locus]] <- L.list[['freq']]
overall.chisq[[Locus]] <- L.list[['chisq']]
ORtable[[Locus]] <- L.list[['OR']]
Final_binned[[Locus]] <- L.list[['table']]
}# END locus loop
Out <- list()
Out[['AB']] <- do.call(rbind,Allele.binned)
Out[['AF']] <- do.call(rbind,Allele.freq)
Out[['CS']] <- do.call(rbind,overall.chisq)
Out[['OR']] <- do.call(rbind,ORtable)
Out[['FB']] <- do.call(rbind,Final_binned)
if(Output) {
## write to file
write.table(Out[['AF']], file = paste("Locus_freqs.txt",sep=""), sep="\t", row.names = F, col.names=T, quote = F)
write.table(Out[['FB']], file = paste("Locus_table.txt",sep=""), sep="\t", row.names = F, col.names=T, quote = F)
write.table(Out[['AB']], file = paste("Locus_binned.txt",sep=""), sep="\t", row.names = F, col.names=T, quote = F)
write.table(Out[['OR']], file = paste("Locus_OR.txt",sep=""), sep="\t", row.names = F, col.names=T, quote = F)
write.table(Out[['CS']], file = paste("Locus_chisq.txt",sep=""), sep="\t", row.names = F, col.names=T, quote = F)
}
cat("> LOCUS LEVEL ANALYSIS COMPLETED","\n")
if(Verbose) {
print(as.data.frame(Out[['CS']]),row.names=F)
cat("\n")
}
return(Out)
}
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