suppressPackageStartupMessages(library(RnBeads))
library(MeDeCom)
options(fftempdir="/scratch/divanshu/dataset1/temp",disk.dump.big.matrices = FALSE,disk.dump.bigff = FALSE)
rnb.options(disk.dump.big.matrices = FALSE,disk.dump.bigff = FALSE)
rnb.set <- load.rnb.set("./2018-07-08_integrated_rnb.clean.RDS.zip")
source("/scratch/divanshu/newset/filtering.R")
res<-prepare_data(
RNB_SET=rnb.set,
WORK_DIR="/scratch/divanshu/dataset1/temp",
DATASET="adgbbSorted",
DATA_SUBSET="frontal",
SAMPLE_SELECTION_COL=NA,
SAMPLE_SELECTION_GREP=NA,
PHENO_COLUMNS=NA,
ID_COLUMN=NA,
NORMALIZATION="none",
REF_CT_COLUMN=NA,
REF_RNB_SET=NA,
REF_RNB_CT_COLUMN=NA,
PREPARE_TRUE_PROPORTIONS=FALSE,
TRUE_A_TOKEN=NA,
HOUSEMAN_A_TOKEN=NA,
ESTIMATE_HOUSEMAN_PROP=FALSE,
FILTER_BEADS=!is.null(rnb.set@covg.sites),
FILTER_INTENSITY=inherits(rnb.set, "RnBeadRawSet"),
FILTER_NA=TRUE,
FILTER_CONTEXT=TRUE,
FILTER_SNP=TRUE,
FILTER_SOMATIC=TRUE,
MATLAB_EXPORT=FALSE
)
rnb.set.filtered <- res$rnb.set.filtered
meth.data <- meth(rnb.set.filtered)
sds<-apply(meth.data, 1, sd)
sortedsdsrownumb <-order(sds, decreasing=TRUE)
sortedsds <- sds[sortedsdsrownumb]
pdf('finalplot.pdf')
plot(sortedsds[1:60000])
dev.off()
cg_subsets <- sortedsdsrownumb[1:20000]
row20k <- list(cg_subsets)
source("/scratch/divanshu/newset/start_analysis.R")
md.res<-start_medecom_analysis(
rnb.set=rnb.set.filtered,
WORK_DIR="/scratch/divanshu/newset/medecomrun",
cg_groups=row20k,
Ks=2:15,
LAMBDA_GRID=c(0,10^(-5:-1)),
SAMPLE_SUBSET=NULL,
K_FIXED=NULL,
WRITE_FILES=FALSE,
startT=NULL,
startA=NULL,
CLUSTER_SUBMIT=FALSE,
CLUSTER_RDIR=NA,
CLUSTER_HOSTLIST="*",
CLUSTER_MEMLIMIT="5G",
# MAX_JOBS=1000,
# WAIT_TIME="30m",
# PORTIONS=FALSE,
# JOB_FILE=NA,
CLEANUP=FALSE
)
saveRDS(md.res,"medecomoutput.rds")
library("FactorViz")
startFactorViz(md.res,input.data=rnb.set.filtered)
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