# Apply a mask to a table of copy number events. A mask is applied to amplified or deleted segments as tabulated in `segtable`. A decision whether to mask a segment is taken based on what portion of the segment is covered by the mask. A position is chosen at random within a segment to be masked, the flanking segments are extended to that position and the segment to be masked is indicated as such in the value returned. ```r applyCNPmask(segtable,chrom,startPos,endPos,startProbe,endProbe, eventIndex,masktable,maskchrom,maskstart,maskend,maskindex,mincover=1, indexvals=c(-1,1)) ``` ## Arguments - `segtable`: A matrix or a data frame with columns named or enumerated by the values of `chrom, startPos, endPos, startProbe, endProbe, eventIndex`. - `chrom`: A character string specifying the name for the column in `segtable` tabulating the (integer) chromosome number for each segment. - `startPos, endPos`: Character strings or integers specifying the names or numbers of columns in `segtable` that tabulate the (integer) genomic start and end coordinates of each segment. - `startProbe, endProbe`: Character strings specifying the names of columns in `segtable` that tabulate the (integer) start and end postions of each segment in internal units such as probe numbers for data of CGH microarray origin. - `eventIndex`: A character string giving the name of a column in `segtable` where copy number variation status of the segments is tabulated. - `masktable`: A matrix or a data frame with columns named or enumerated as given by `maskchrom, maskstart, maskend, maskindex` and with rows corresponding to genomic intervals that comprise the mask. - `maskchrom,maskstart,maskend`: Character strings or integers specifying the names or numbers of columns in `masktable` that tabulate the chromosome number and (integer) genomic start and end coordinates of the intervals comprising the mask. - `maskindex`: A numeric vector corresponding to `eventIndex`,specifying copy number events status for measuring units. - `mincover`: A numeric value specifying the minimal portion of the segment that must be covered by the mask in order to trigger masking. - `indexvals`: A numeric vector of length 2 specifying the two values in `maskindex` to be matched with values in `eventIndex` to determine the events that are to be masked. ## Details Masking is performed separately for each value in `indexvals`. Segments (rows of `segtable`) with that value of `eventIndex` are examined for coverage by mask intervals with that value of `maskindex` in `masktable`. If the coverage is at least `mincover`, the segment is slated for masking, while its flanking segments are extended to a random point within the segment being masked. ## Returns A matrix with same number of observations/rows as `segtable` and with following three columns: - **startProbe,endProbe**: An integer vector for the start and end positions of the segments after masking. - **toremove**: An integer vector whose values are 1 if the segment is masked and 0 otherwise. ## Author(s) Alex Krasnitz ## Examples ```r ## Not run: data(segexample) data(ratexample) data(normsegs) data(cnpexample) segtable<-CNpreprocessing(segall=segexample[segexample[,"ID"]=="WZ1",], ratall=ratexample,"ID","start","end",chromcol="chrom",bpstartcol="chrom.pos.start", bpendcol="chrom.pos.end",blsize=50,minjoin=0.25,cweight=0.4,bstimes=50, chromrange=1:22,distrib="Rparallel",njobs=2,modelNames="E",normalength=normsegs[,1], normalmedian=normsegs[,2]) #form a eventIndex vector eventIndex<-rep(0,nrow(segtable)) eventIndex[segtable[,"marginalprob"]<1e-4&segtable[,"negtail"]> 0.999&segtable[,"mediandev"]<0] <- -1 eventIndex[segtable[,"marginalprob"]<1e-4&segtable[,"negtail"]> 0.999&segtable[,"mediandev"]>0] <- 1 segtable<-cbind(segtable,eventIndex) #form a cnpindex vector namps17<-cnpexample[cnpexample[,"copy.num"]=="amp",] aCNPmask<-makeCNPmask(imat=namps17,chromcol=2,startcol=3,endcol=4, nprof=1203,uthresh=0.02,dthresh=0.008) ndels17<-cnpexample[cnpexample[,"copy.num"]=="del",] dCNPmask<-makeCNPmask(imat=ndels17,chromcol=2,startcol=3,endcol=4, nprof=1203,uthresh=0.02,dthresh=0.008) cnptable<-rbind(cbind(aCNPmask,cnpindex=1),cbind(dCNPmask,cnpindex=-1)) #run the CNP test myCNPtable<-applyCNPmask(segtable,"chrom",startPos="chrom.pos.start", endPos="chrom.pos.end","start","end","eventIndex",masktable=cnptable,"chrom", maskstart="start",maskend="end",maskindex="cnpindex",mincover=0.005,indexvals=c(-1,1)) ## End(Not run) ```

applyCNPmask function