Hi everyone, I am looking at coverage in certain continuous intervals of a gene.I have got this Views object. However Could I do normalization of the reads  in this object which is very necessary in doing any analysis further? ir <- IRanges(c(90645249,90645349,90645449,90645549,90645649,90645749, 90645849,90645949,90646049,90646149,90646249,90646349,90646449,9064654 9,90646649,90646749, 90646849,90646949,90647049,90647149,90647249,90647349,90647449,9064754 9,90647649,90647749),width=100) gr <- GRanges(seqnames = "chr4", ranges = ir,strand = "-") grl<- as(gr,"RangesList") cov4 <- cover[29] ##subsetting coverage for chr4 vl <- Views(cov4,grl) vl SimpleRleViewsList of length 1 $chr4 Views on a 191154276-length Rle subject views:         start      end width  [1] 90645249 90645348   100 [  2  10  33  41  52  81  99 117 132 157 223 ...]  [2] 90645349 90645448   100 [1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...]  [3] 90645449 90645548   100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...]  [4] 90645549 90645648   100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...]  [5] 90645649 90645748   100 [1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 ...]  [6] 90645749 90645848   100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...]  [7] 90645849 90645948   100 [1 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 ...]  [8] 90645949 90646048   100 [4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 ...]  [9] 90646049 90646148   100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...]  ...      ...      ...   ... ... [18] 90646949 90647048   100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] [19] 90647049 90647148   100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] [20] 90647149 90647248   100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] [21] 90647249 90647348   100 [433 433 433 433 433 433 433 433 433 433 433 ...] [22] 90647349 90647448   100 [40 40 40 40 40 40 40 40 40 40 37 35 34 28 ...] [23] 90647449 90647548   100 [4 4 4 4 4 4 3 3 2 1 0 0 0 0 0 0 0 0 0 0 0 0 ...] [24] 90647549 90647648   100 [27 27 27 27 27 27 27 27 26 25 24 24 24 23 ...] [25] 90647649 90647748   100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] [26] 90647749 90647848   100 [2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 0 0 0 0 0 0 ...] I would really appreciate any ideas.. Thanks, Rohan [[alternative HTML version deleted]]

It sounds like you want to apply a normalization function to each of the coverage views. This can be done with sapply (or lapply). If you have a function called 'normalize' you want to apply to the coverage, sapply(vl, normalize) See ?sapply or try a simple example, sapply(vl, sum) to get an idea of how it works. Valerie On 11/02/2011 12:24 PM, rohan bareja wrote: > > > > Hi everyone, > > I am looking at coverage in certain continuous intervals of a gene.I have got this Views object. > However Could I do normalization of the reads in this object which is very necessary in doing any analysis further? > > ir<- IRanges(c(90645249,90645349,90645449,90645549,90645649,90645749 ,90645849,90645949,90646049,90646149,90646249,90646349,90646449,906465 49,90646649,90646749, > 90646849,90646949,90647049,90647149,90647249,90647349,90647449,90647 549,90647649,90647749),width=100) > > gr<- GRanges(seqnames = "chr4", ranges = ir,strand = "-") > grl<- as(gr,"RangesList") > > > cov4<- cover[29] ##subsetting coverage for chr4 > > vl<- Views(cov4,grl) > > vl > SimpleRleViewsList of length 1 > $chr4 > Views on a 191154276-length Rle subject > > views: > start end width > [1] 90645249 90645348 100 [ 2 10 33 41 52 81 99 117 132 157 223 ...] > [2] 90645349 90645448 100 [1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] > [3] 90645449 90645548 100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] > [4] 90645549 90645648 100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] > [5] 90645649 90645748 100 [1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 ...] > [6] 90645749 90645848 100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] > [7] 90645849 90645948 100 [1 2 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 ...] > [8] 90645949 90646048 100 [4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 ...] > [9] 90646049 90646148 100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] > ... ... ... ... ... > [18] 90646949 90647048 100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] > [19] 90647049 90647148 100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] > [20] 90647149 90647248 100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] > [21] 90647249 90647348 100 [433 433 433 433 433 433 433 433 433 433 433 ...] > [22] 90647349 90647448 100 [40 40 40 40 40 40 40 40 40 40 37 35 34 28 ...] > [23] 90647449 90647548 100 [4 4 4 4 4 4 3 3 2 1 0 0 0 0 0 0 0 0 0 0 0 0 ...] > [24] 90647549 90647648 100 [27 27 27 27 27 27 27 27 26 25 24 24 24 23 ...] > [25] 90647649 90647748 100 [0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...] > [26] 90647749 90647848 100 [2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 1 0 0 0 0 0 0 ...] > > > I would really appreciate any ideas.. > > > Thanks, > Rohan > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

Hi Valerie, Thats what I wanted to do but I dont know how to write a normalization function for Coverage.. Would it be somewhat calculating RPKMs ??If yes how should I do that? Thanks, Rohan [[alternative HTML version deleted]]