sample.conf

#Customize variables here:######################################################
################################################################################

#Load the files:
#
infiles       <- setup_BWASPR(datafile="../inst/extdata/AmHE.dat",
                              parfile="../inst/extdata/AmHE.par")

#Set the study and samples in the study:
#
species       <- "Am"
study         <- "HE"
samplelist    <- list("forager","nurse")
## The following two variables are used for output file labeling:
studyLabel    <- "HE"
sampleLabels  <- list("Am_HE_fr","Am_HE_rn")

hasreplicates <- FALSE
type          <- "CpG"
destrand      <- TRUE
covlist       <- c(6,20,50)
locount       <- 100
hicount       <- 1000
repcovlist    <- c(6,10,15)
replocount    <- 10
rephicount    <- 100
hheight       <- 0.120
nbrpnts       <- 5000

## The following four variables are sent to rank_rbm() and determine what data
#  points get plotted:
minnbrmsprm   <- 5	# minimum number of methylation sites per promoter
mingenewidth  <- 500	# minimum gene width
maxgenewidth  <- 5000	# maximum gene width
minnbrmsgene  <- 5	# minimum number of methylation sites per gene

## Other parameters (see Rscript.BWASPR for usage notes):
#
filter.lo.count <- NULL	# option to MethylKit::filterByCoverage prior to CRL analysis
filter.lo.perc  <- NULL	# option to MethylKit::filterByCoverage prior to CRL analysis
filter.hi.count <- NULL	# option to MethylKit::filterByCoverage prior to CRL analysis
filter.hi.perc  <- NULL	# option to MethylKit::filterByCoverage prior to CRL analysis
highcoverage  <- 20	# high read coverage threshold for studyhc methylRawList object
threshold     <- 20.0	# "difference" threshold for getMethylDiff(), called by det_dmsg()
qvalue        <- 0.05	# "qvalue" setting for getMethylDiff(), called by det_dmsg()
wsize         <- 500	# "win.size" parameter for tileMethylCounts() in det_dmt()
stepsize      <- 500	# "step.size" parameter for tileMethylCounts() in det_dmt()

minNsites     <-  1	# minimum number of hc sites in a gene to be heatmapped in show_dmsg()
maxNsites     <- 60	# maximum number of hc sites in a gene to be heatmapped in show_dmsg()
minPdmsites   <- 10	# minimum ratio of dm/hc (in %) in a gene to be heatmapped in show_dmsg()

maxgwidth     <- 20000	# maximal gene width for a gene to be considered by explore_dmsg()
minnbrdmsites <- 1    	# minimum number of differentially methylated sites for a gene to be
                        #  considered in sample comparisons by explore_dmsg()
glink         <- "NCBIgene"	# URL to show in explore_dmsg(); options: "" or "NCBIgene"

#Set the number of processors to use:
#
numprc <-  4

#Determine what analyses to run:
#
RUNload    <- FALSE

RUNcms     <- TRUE
RUNpwc     <- TRUE
RUNcrl     <- TRUE

RUNrepcms  <- TRUE
RUNrepcrl  <- TRUE

RUNmmp     <- TRUE
RUNacs     <- TRUE
RUNrnk     <- TRUE
RUNmrpr    <- TRUE

RUNdmt     <- TRUE
RUNdmsg    <- TRUE
RUNdmgdtls <- TRUE
RUNogl     <- TRUE

RUNsave    <- FALSE


mymessage <- sprintf("\nAnalyzing %s study %s for type %s\n\n",species,studyLabel,type)
message(mymessage)

################################################################################
#End of typical customization.##################################################