bug fix: fixed rcMethlvl file and dataread

.gitignore

@@ -4,6 +4,7 @@
 .Ruserdata
 .Rbuildignore
 .Rproj
+*.Rproj
 inst/doc
 .renviron
 .rprofile

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: AlphaBeta
 Type: Package
 Title: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
-Version: 1.2.1
+Version: 1.2.2
 Authors@R: c(
     person("Yadollah", "Shahryary Dizaji", email = "[email protected]", role = c("cre","aut")),
     person("Frank", "Johannes", email = "[email protected]", role = "aut"),

R/D-matrices.R

@@ -104,12 +104,4 @@ runMatrix <- function(pairs, cytosine, posteriorMaxFilter,genTable){
     return(tmp_big)
 }
 
-#dMsaveResult<-function(final_ds,cytosine,posteriorMaxFilter){
-#    cat("Writing to the files:\n")
-#    final_ds<-final_ds[mixedorder(final_ds$X1),]
-#    colnames(final_ds)<-(c("pair.1", "pair.2", "D.value"))
-#    saved_file <- paste0(getwd(), "/", "AB-dMatrix-", cytosine, "-", posteriorMaxFilter, ".csv")
-#    fwrite(final_ds, file = saved_file , quote = FALSE, sep = '\t', row.names = FALSE, col.names = TRUE)
-#    cat(paste0("Divergence values saved in: ",saved_file, "\n"))
-#}
 

R/rcMethlvl.R

@@ -29,7 +29,6 @@ rc.meth.lvl <- function(nodelist, cytosine, posteriorMaxFilter){
       #---------------------------Filter based on WGBS
       genTable <- genTable %>% filter(genTable$meth=="Y")
       #---------------------------
-
       list.rc<-bplapply(genTable$filename,cytosine=cytosine,posteriorMaxFilter= posteriorMaxFilter,
         genTable= genTable, rcRun, BPPARAM = SnowParam(exportglobals = FALSE))