On Wed, Mar 17, 2010 at 10:15 AM, Zhu, Julie <[email protected]> wrote:
> Thanks, Michael! > > Would you recommend RangedDataList over list(peaks1, peaks2)? Thanks! > > Yes. It should behave similarly, and verifies that each element is indeed a RangedData. Best, > > Julie > > > > On 3/17/10 12:12 PM, "Michael Lawrence" <[email protected]> wrote: > > RangedData is a vector or list-like object, so concatenating will behave as > with other such objects. There is however a RangedDataList. Try > RangedDataList(peaks1, peaks2). > > Michael > > On Wed, Mar 17, 2010 at 10:00 AM, Zhu, Julie <[email protected]> > wrote: > > Hi, > > I want to pass in a vector of RangedData to a function. But the vector > became one combined RangedData. > > Here is an example with two RangedData. > > peaks1= RangedData(IRanges(start = c(967654, 2010897, 2496704), end = > c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")), space = > c("1", "2", "3"), strand=as.integer(1)) > > peaks2 = RangedData(IRanges(start = c(967659, 2010898, 2496700, 3075866, > 3123260), end = c(967869, 2011108, 2496920, 3076166, 3123470), names = > c("t1", "t2", "t3", "t4", "t5")), space = c("1", "2", "3", "1", "2"), > strand > = c(1, 1, -1,-1,1)) > > Peaks=c(peaks1,peaks2) > > Now Peaks become one RangedData. Is there a way to create a vector of > RangedData without combining all the RangedData into one? Thanks! > > RangedData with 10 rows and 1 value column across 4 spaces > space ranges | strand > <character> <IRanges> | <integer> > p5 5 [167889600, 167893599] | 1 > p1 6 [ 1543200, 1555199] | 1 > p2 6 [ 1557200, 1560599] | 1 > p3 6 [ 1563000, 1565199] | 1 > p4 6 [ 1569800, 1573799] | 1 > f5 5 [167888600, 167888999] | 1 > f1 6 [ 1549800, 1550599] | 1 > f2 6 [ 1554400, 1560799] | 1 > f3 6 [ 1565000, 1565399] | 1 > f4 6 [ 1569400, 1571199] | 1 > > Here is the session information. > > sessionInfo() > R version 2.10.0 (2009-10-26) > i386-apple-darwin8.11.1 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ChIPpeakAnno_1.2.8 limma_2.19.2 > org.Hs.eg.db_2.3.6 > [4] GO.db_2.3.5 RSQLite_0.7-1 > DBI_0.2-4 > [7] AnnotationDbi_1.8.1 > BSgenome.Ecoli.NCBI.20080805_1.3.16 > BSgenome_1.14.2 > [10] Biostrings_2.14.8 IRanges_1.4.9 > multtest_2.1.2 > [13] Biobase_2.5.5 biomaRt_2.1.0 > > loaded via a namespace (and not attached): > [1] MASS_7.3-3 RCurl_0.98-1 splines_2.10.0 survival_2.35-7 > tools_2.10.0 XML_2.3-0 > > Best regards, > > Julie > > > ******************************************* > Lihua Julie Zhu, Ph.D > Research Associate Professor > Program Gene Function and Expression > University of Massachusetts Medical School > 364 Plantation Street, Room 613 > Worcester, MA 01605 > 508-856-5256 > http://www.umassmed.edu/pgfe/faculty/zhu.cfm > ******************************************* > > > > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
