Thanks Michael! I did do summaries. However, I am more interested in the positional distribution of the counts across the region encompassed by the islands. Let me explore viewApply.
-Best -Lax Sent from my iPhone On Apr 14, 2011, at 10:41 AM, Michael Lawrence <lawrence.mich...@gene.com> wrote: > Generally, people summarize the coverage in each island, like with viewSums, > viewMaxs, etc. For other, custom summaries, see viewApply (but this is not > optimized like the others). > > Michael > > On Thu, Apr 14, 2011 at 7:19 AM, Lakshmanan Iyer <lax...@gmail.com> wrote: > Hi > I have calculated coverage and islands of coverage from a filtered set of > alignments from a bam file using Bioconductor tools. I finally got the > islands but am stuck with how to extract the individual coverage at each > position on the islands. Any help is appreciated. Details below: > ..... > cov <- coverage(filtData2) > islands <- slice (cov, lower=1); > .... > > > islands > SimpleRleViewsList of length 22 > $chr1 > Views on a 196923949-length Rle subject > > views: > start end width > [1] 3204937 3205007 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > ...] > [2] 3205421 3205491 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > ...] > [3] 4886462 4886532 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > ...] > [4] 4887255 4887325 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > ...] > [5] 6849632 6849852 221 [1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 > ...] > [6] 7160418 7160488 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > ...] > [7] 7160629 7160699 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > ...] > [8] 7160746 7160816 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > ...] > [9] 7160832 7160902 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > ...] > ... ... ... ... ... > [1186] 196640431 196640663 233 [ 1 1 1 2 4 4 4 5 5 5 5 5 5 > ...] > [1187] 196640859 196641155 297 [3 5 5 6 6 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 > ...] > [1188] 196641193 196641265 73 [1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 > ...] > > I was wondering how one could get the coverage values out of this > SimpleRleViewsList (see below) > I could get the dataframe and he named columns, see > > space start end width > 1 chr1 3204937 3205007 71 > 2 chr1 3205421 3205491 71 > 3 chr1 4886462 4886532 71 > > but would like to get the coverage at each position so that I can use it do > some more analysis > > [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...] > > Any clues? > -best > -Lax > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
