R/hz.cracker.default.settings.R

In cRacker: R-script suite for automated processing of proteomic peptide lists

hz.cracker.default.settings <-
function(){
	return(

settings <- list(	tb1.val.replicates 		= "1",
					tb1.val.replicates.cp	= "0",
					tb1.var.protein.intensity =	"median",
					tb1.duplicates.var			= "max",
					tb1.val.conrev			= "1",
					val.norm.method			= "1",
					tb2.norm.method		= "median",
					
					tb2.val.score			= 20,
					tb2.var.rownorm			= "1",
					tb2.var.shape			= "50",
					tb2.var.red.pep			= "0",
					tb2.var.db				= "Arabidopsis_20110903",
					tb2.var.red.pep.mq		= "0",
					tb2.var.groupnorm		= "0",
					tb2.var.group.filternorm = "0",
					
					
					tb3.var.phospho			= "none",
					tb3.var.info			= "1",
					tb3.outlier				= "none",
					tb3.val.outlier			= "1",
					tb3.val.zero.treat		= "NA",
					
					tb4.quant.method		= "lf",
					tb4.val.raw.values 		= "fraction of total",
					tb4.var.cbn				= "0",
					tb4.var2.cbn			= "0",
					tb4.val.cbn.prot		= "CON_P02769",
					tb4.val.cbn.shape		= "100",
					tb4.val.n15				= "0",
					tb4.val.n15.log			= "0",
					tb4.var.n15.log.correction	= "none",
					tb4.val.ratio 			= "1",
					
					tb5.val.kmeans 			= "auto",
					tb5.val.anova.p			= "0.01",
					tb5.var.p.adjust		= "BH",
					tb5.var.do.go			= "1",
					tb5.go.term.list		= "Ath-AGI-TAIR9-Jan2010-cut3",
					tb5.var.do.network		= "0",
					tb5.do.cor				= "pearson",
					tb5.var.color.plots		= "rainbow",
					tb5.val.volcano			= "1",
					tb5.var.graphic.type	= "pdf",
					tb5.var.log2.ratio.thres= "0.5",
					tb5.nb.2.fl.bp.frame.val.plot.type = "barplot",
					tb5.nb.2.fl.bp.frame.var.xlab	= "time",
					tb5.val.cluster.method	= "hclust",
					tb5.val.anova.log2		= "1",
					val.onetailed.ttest		= "1",
					
					tb6.var.shape.script	= "0",
					path4 					= "",
					tt2.settings.var		= "current settings",
					
					tb1.calc.empai			= "0",
					tb1.empai.sd			= "0",
					tb1.empai.from.msms		= "1",
					tb1.empai.ref.list		= "Arabidopsis_20110903",
					tb1.empai.pep.length	= 6	
				)
				)
				}