#
# Neuronal data from Gasparoni et al., 2017
#
.libPaths("/DEEP_fhgfs/projects/plutsik/Rlib_clean_RnBeads/")
PROJECT.DIR="/DEEP_fhgfs/projects/plutsik/projects/neuron/"
data<-read.table(file.path(PROJECT.DIR, "20170419_GasSort_GuiSort_manuscriptData.txt"))
pd<-read.table(file.path(PROJECT.DIR, "20170419_GasSort_GuiSort_manuscriptSampleSheet.txt"), sep='\t', header=TRUE)
probe.list<-rownames(data)
library(RnBeads)
rnb.options(disk.dump.big.matrices=FALSE)
rnb.set<-RnBeadSet(pd, probe.list, as.matrix(data))
#### neuron
res<-prepare_data(
RNB_SET=rnb.set,
WORK_DIR=file.path(PROJECT.DIR),
DATASET="adgbbSorted",
DATA_SUBSET="neuron",
SAMPLE_SELECTION_COL="Celltype",
SAMPLE_SELECTION_GREP="Neuron",
PHENO_COLUMNS=NA,
ID_COLUMN=NA,
NORMALIZATION="custom",
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=TRUE
)
res_selection<-prepare_CG_subsets(
res$rnb.set.filtered,
MARKER_SELECTION=c("var10k", "var50k"),
WD=file.path(PROJECT.DIR),
analysis_info=res$info
)
md.res<-start_medecom_analysis(
rnb.set=res$rnb.set.filtered,
WORK_DIR=file.path(PROJECT.DIR),
cg_groups=res_selection$cg_groups,
Ks=2:10,
LAMBDA_GRID=c(0,10^(-5:-1)),
SAMPLE_SUBSET=NULL,
K_FIXED=NA,
WRITE_FILES=TRUE,
startT=NULL,
startA=NULL,
NINIT=10,
ITERMAX=300,
NFOLDS=9,
N_COMP_LAMBDA=4,
NCORES=10,
OPT_METHOD="cppTAfact",
CLUSTER_SUBMIT=FALSE,
CLUSTER_RDIR=NA,
CLUSTER_HOSTLIST="*",
CLUSTER_MEMLIMIT="5G",
# MAX_JOBS=1000,
# WAIT_TIME="30m",
# PORTIONS=FALSE,
# JOB_FILE=NA,
CLEANUP=FALSE,
analysis_info=res_selection$info
)
saveRDS(md.res, file="/DEEP_fhgfs/projects/plutsik/projects/neuron/md.res.neuron.var10k.var50k_new.RDS")
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