Thanks, Michael!

Would you recommend RangedDataList over list(peaks1, peaks2)? Thanks!

Best,

Julie


On 3/17/10 12:12 PM, "Michael Lawrence" <lawrence.michael@gene.com> 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 <Julie.Zhu@umassmed.edu> 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
*******************************************






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