Hi Abirami,

Your file is not in bed file format. Please check out the bed file format definition at http://genome.ucsc.edu/FAQ/FAQformat.html#format1. The orders of the columns are important. In addition, currently BED2RangedData uses the name column as rownames of the RangedData which needs to be unique. If the name column is missing, BED2RangedData will assign rownames automatically.

Here is an example.
test.bed = data.frame(cbind(chrom = c("1", "2"), chromStart=c("100", "1000"),chromEnd=c("200", "1100"), name=c("peak1", "peak2")))
test.rangedData = BED2RangedData(test.bed)

Please type ?BED2RangedData in a R session for more details. BTW, it would be helpful to include the    session information for future correspondence.

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



On 4/20/10 3:48 PM, "Abirami Subbu" <abi.bio.86@gmail.com> wrote:

          name chromStart chromEnd strand            chrom
1     NM_001001398   13196926 13203469     -1            chr25
2     NM_001001399    4025604  4033166     -1            chr19
3     NM_001001401   12007237 12036869      1            chr14
4     NM_001001402    8387701  8401691      1            chr22
5     NM_001001403    6729898  6782124     -1             chr3
6     NM_001001406   39498223 39506396      1            chr19
7     NM_001001407    3585650  3602600     -1            chr15
8     NM_001001409   38023452 38029815      1            chr20
9     NM_001001501    3187183  3217911     -1             chr6

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