inst/unitTests/sequencing_test.R

In lutsik/DecompPipeline: Preparation pipeline for MeDeCom

library(devtools)
devtools::install_local("/TL/deep/projects/work/mscherer/projects/MeDeCom/DecompPipeline/",lib="/TL/deep/projects/work/mscherer/projects/RnBeads/R/cleaner_lib/")
  library(DecompPipeline)

options(fftempdir="/DEEP_fhgfs/projects/mscherer/deep/tmp")  
  rnb.set <- load.rnb.set("/DEEP_fhgfs/projects/mscherer/data/RRBS/mouse/brahamMouse2017/report/rnbSet_unnormalized/")
  work.dir <- "/TL/deep/projects/work/mscherer/projects/MeDeCom/test/prepare_BS"
  analysis.name <- "TestBS"
  
#   data.prep <- prepare_data_BS(rnb.set,
#                                WORK_DIR=work.dir,
#                                analysis.name=analysis.name)
# 
# subsets <- prepare_CG_subsets(
# 	data.prep$rnb.set.filtered,
# 	MARKER_SELECTION=c("pheno","random","pca","var","hybrid","range"),
# 		WD=file.path(work.dir,"data","foo_foo_none"),
# 		N_MARKERS = 4242,
# 		N_PRIN_COMP = 2,
# 		RANGE_DIFF = 0.1
# )

md.res <- start_decomp_pipeline(
  rnb.set = rnb.set,
  Ks = 2,
  lambda=0,
  work.dir = work.dir,
  analysis.name = analysis.name
)