@@ -1,7 +1,7 @@

 Package: scmeth

 Type: Package

 Title: Functions to conduct quality control analysis in methylation data

-Version: 0.99.29

+Version: 0.99.30

 Author: Divy Kangeyan <[email protected]>

 Maintainer: Divy Kangeyan <[email protected]>

 Depends: R (>= 3.5.0)

@@ -50,16 +50,17 @@ mbiasplot <- function(dir=NULL,mbiasFiles=NULL){

     mbiasTable <- rbind(CpG_Mbias_Read1[,c('position','X..methylation','read')],

                         CpG_Mbias_Read2[,c('position','X..methylation','read')])

+    colnames(mbiasTable)<-c('position','methylation','read')

     mbiasTableList[[i]] <- mbiasTable

     }

     mt <- reshape2::melt(mbiasTableList,

-                        id.vars=c('position', 'X..methylation', 'read'))

+                        id.vars=c('position', 'methylation', 'read'))

     mt$read_rep <- paste(mt$read, mt$L1, sep="_")

-    meanTable <- stats::aggregate( X..methylation ~ position+read, data=mt, FUN=mean)

-    sdTable <- stats::aggregate( X..methylation ~ position+read, data=mt, FUN=sd)

-    seTable <- stats::aggregate( X..methylation ~ position+read, data=mt, FUN=function(x){sd(x)/sqrt(length(x))})

+    meanTable <- stats::aggregate( methylation ~ position+read, data=mt, FUN=mean)

+    sdTable <- stats::aggregate( methylation ~ position+read, data=mt, FUN=sd)

+    seTable <- stats::aggregate( methylation ~ position+read, data=mt, FUN=function(x){sd(x)/sqrt(length(x))})

     sum_mt<-data.frame('position'=meanTable$position,'read'=meanTable$read,

                        'meth'=meanTable$X..methylation, 'sdMeth'=sdTable$X..methylation,