modified the ranking function and added TopDAClonotypes function

R/RepDaAnalysisFns.R

@@ -2259,7 +2259,7 @@ runDaAnalysis <- function(repSeqObj,clusterby="NT",kmerWidth=4,paired=T,clusterD
 #' @param pValueCutoff the cutoff p-value, default is 0.05
 #' @return function returns a data frame of the candidate CDR3s that have significant p-value, that is below the pValueCutoff
 #' 
-#' @example TopDAClonotypes(results,enriched=T,pValueCutoff=T) # results is an object holding the result of running runDaAnalysis
+#' @example TopDAClonotypes(results,enriched=T,pValueCutoff=0.05) # results is an object holding the result of running runDaAnalysis
 #' 
 #' @export
 #' 

README.md

@@ -48,13 +48,13 @@ results <- runDaAnalysis(repObj,clusterby="NT",kmerWidth=4,paired=T,clusterDaPcu
 Significantly differentially enriched CDR3s (with permuted p-values < 0.05), that have shown significant clonal expansion in condition 2, can be accessed from the result using :
 
 ```
-enriched <- results[[1]][results[[1]]$permutedEnPval < 0.05,]
+enrichedCDR3s <- TopDAClonotypes(results,enriched=T,pValueCutoff=0.05)
 ```
 
 Significantly differentially de-enriched CDR3s (with permuted p-values < 0.05), that have shown significant clonal contraction in condition 2, can be accessed from the result using :
 
 ```
-de-enriched <- results[[1]][results[[1]]$permutedDeEnPval < 0.05,]
+de-enrichedCDR3s <- TopDAClonotypes(results,enriched=F,pValueCutoff=0.05)
 ```