Entering edit mode
Hi Eric,
You have NA in your name column. One fix for you without creating a
name
column is to just use the following code to create RangedData from
your
dataframe.
RangedData(Iranges(start=as.numeric(as.character(TwoLplus[,2])),
end=as.numeric( as.character(TwoLplus[,3])),names=paste(TwoLplus[,1],
TwoLplus[,2], TwoLplus[,3])), space= as.character(TwoLplus[,1]),
strand=
as.character(TwoLplus[,6]))
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 2/26/10 3:20 PM, "Eric Bremer" <ericgbremer@gmail.com> wrote:
> Hi Julie,
> Thanks so much for your help so far. I have been trying to convert
some of my
> data from a BED format into the ranged data and seem to run into a
couple of
> errors that I can not seem to fix. Here is an example:
>
>> > TwoLplus = read.table("2Lplus_bed2.txt", header=TRUE, sep="\t",
fill=TRUE)
>> > test = BED2RangedData(TwoLplus, header=TRUE)
> Error in `rownames<-`(`*tmp*`, value = c(NA_character_,
NA_character_, :
> missing values not allowed in rownames
> In addition: Warning messages:
> 1: In `[<-.factor`(`*tmp*`, strand == "+", value = 1) :
> invalid factor level, NAs generated
> 2: In `[<-.factor`(`*tmp*`, strand == "-", value = -1) :
> invalid factor level, NAs generated
>> > head(TwoLplus)
> chrom peakStart peakEnd name score strand
> 1 chr2L 9115 9140 NA NA +
> 2 chr2L 9410 9489 NA NA +
> 3 chr2L 12342 12368 NA NA +
> 4 chr2L 25256 25281 NA NA +
> 5 chr2L 27909 27934 NA NA +
> 6 chr2L 30731 30756 NA NA +
>> >
>
>
> I have also attached the origninal .txt file that I am starting
with. I
> suspect that I am missing something simple (at least I hope so)
> Thanks!
> Eric
[[alternative HTML version deleted]]