From 601fa96449e4c63b2326fb3a60645d88c5a55c04 Mon Sep 17 00:00:00 2001 From: Yadi Date: Wed, 3 Jun 2020 09:23:37 +0200 Subject: [PATCH] bug fix: fixed rcMethlvl file and dataread --- .gitignore | 1 + DESCRIPTION | 2 +- R/D-matrices.R | 8 -------- R/rcMethlvl.R | 1 - 4 files changed, 2 insertions(+), 10 deletions(-) diff --git a/.gitignore b/.gitignore index 54f09c2..f370c1a 100644 --- a/.gitignore +++ b/.gitignore @@ -4,6 +4,7 @@ .Ruserdata .Rbuildignore .Rproj +*.Rproj inst/doc .renviron .rprofile diff --git a/DESCRIPTION b/DESCRIPTION index a2eda13..a965329 100644 --- a/DESCRIPTION +++ b/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 = "shahryary@gmail.com", role = c("cre","aut")), person("Frank", "Johannes", email = "frank@jlab.org", role = "aut"), diff --git a/R/D-matrices.R b/R/D-matrices.R index 9bb76d9..897d6e3 100644 --- a/R/D-matrices.R +++ b/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$X1),] -# colnames(final_ds)<-(c("pair.1", "pair.2", "D.value")) -# saved_file <- paste0(getwd(), "/", "AB-dMatrix-", cytosine, "-", posteriorMaxFilter, ".csv") -# fwrite(final_ds, file = saved_file , quote = FALSE, sep = '\t', row.names = FALSE, col.names = TRUE) -# cat(paste0("Divergence values saved in: ",saved_file, "\n")) -#} diff --git a/R/rcMethlvl.R b/R/rcMethlvl.R index 01ced1e..ac3ba2e 100644 --- a/R/rcMethlvl.R +++ b/R/rcMethlvl.R @@ -29,7 +29,6 @@ rc.meth.lvl <- function(nodelist, cytosine, posteriorMaxFilter){ #---------------------------Filter based on WGBS genTable <- genTable %>% filter(genTable$meth=="Y") #--------------------------- - list.rc<-bplapply(genTable$filename,cytosine=cytosine,posteriorMaxFilter= posteriorMaxFilter, genTable= genTable, rcRun, BPPARAM = SnowParam(exportglobals = FALSE))