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

 Package: scmeth

 Type: Package

 Title: Functions to conduct quality control analysis in methylation data

-Version: 0.99.26

+Version: 0.99.27

 Author: Divy Kangeyan <[email protected]>

 Maintainer: Divy Kangeyan <[email protected]>

 Depends: R (>= 3.5.0)

@@ -26,7 +26,7 @@ Imports:

   scales,

   viridis,

   magrittr,

-  dplyr,

+  plyr,

   HDF5Array (>= 1.7.5)

 Suggests:

   BSgenome.Mmusculus.UCSC.mm10,

@@ -13,7 +13,6 @@

 #'library(BSgenome.Hsapiens.NCBI.GRCh38)

 #'directory <- system.file("extdata/bismark_data",package='scmeth')

 #'bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)

-#'memory.limit(size=300)

 #'cpgDensity(bs,Hsapiens,1000,small=TRUE)

 #'@import BSgenome

 #'@importFrom bsseq getCoverage

@@ -14,6 +14,8 @@

 #'@importFrom utils read.table

 #'@importFrom utils read.csv

 #'@importFrom stats sd

+#'@importFrom summarise plyr

+#'@importFrom ddply plyr

 #'@import magrittr

 #'@export

@@ -56,10 +58,14 @@ mbiasplot <- function(dir=NULL,mbiasFiles=NULL){

     mt <- reshape2::melt(mbiasTableList,

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

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

-    sum_mt <- mt %>% dplyr::group_by(position,read) %>%

-                        dplyr::summarise(meth = mean(X..methylation),

-                                sdMeth=stats::sd(X..methylation))

-    sum_mt$seMeth <- sum_mt$sdMeth/sqrt(nSamples)

+

+    sum_mt <- plyr::ddply(mt, c("position", "read"), plyr::summarise,

+                    meth = mean(X..methylation), sdMeth = sd(X..methylation),

+                    seMeth = sd(X..methylation)/sqrt(length(X..methylation)))

+    #sum_mt <- mt %>% dplyr::group_by(position,read) %>%

+                        #dplyr::summarise(meth = mean(X..methylation),

+                           #     sdMeth=stats::sd(X..methylation))

+    #sum_mt$seMeth <- sum_mt$sdMeth/sqrt(nSamples)

     sum_mt$upperCI <- sum_mt$meth+(1.96*sum_mt$seMeth)

     sum_mt$lowerCI <- sum_mt$meth-(1.96*sum_mt$seMeth)

     sum_mt$read_rep <- paste(sum_mt$read, sum_mt$position,sep="_")

@@ -31,6 +31,5 @@ of CpGs observed in certain base pair long region.

 library(BSgenome.Hsapiens.NCBI.GRCh38)

 directory <- system.file("extdata/bismark_data",package='scmeth')

 bs <- HDF5Array::loadHDF5SummarizedExperiment(directory)

-memory.limit(size=300)

 cpgDensity(bs,Hsapiens,1000,small=TRUE)

 }