
Hi everyone,
I am looking at coverage in certain intervals of a chromosome.I have got this Views object.However Could I do normalization of the reads  which is very necessary in doing any analysis further?
ir <- IRanges(c(90645249,90645349,90645449,90645549,90645649,90645749,90645849,90645949,90646049,90646149,90646249,90646349,90646449,90646549,90646649,90646749,90646849,90646949,90647049,90647149,90647249,90647349,90647449,90647549,90647649,90647749),width=100)gr <- GRanges(seqnames = "chr4", ranges = ir,strand = "-")
cov <- cover[29] ##subsetting coverage for chr4
vl <- Views(cov4,grl)
vlSimpleRleViewsList of length 1$chr4Views 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 ...]



Thanks,Rohan


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