[BioC] tilingArray - plotAlongChrom problem

[Krys Kelly]

I have data from a 650kb section of a chromosome on a tiling array. 

When I run a segmentation and try to plot the results along the chromosome I
get the following error:

 > plotAlongChrom(segObj, chr=1, coord=c(1, 100000), gff=gff)
Error in get(x, envir, mode, inherits) : variable "1.-.dat" was not found

Here is my code:

INFILE  <- "RH_i_vs_cell.txt"
GFFFILE <- "t_gondii_ME49_Ib_650kb.gff"

array <- read.table(INFILE, header=TRUE)
gff   <- read.table(GFFFILE, header=TRUE)

# maxseg corresponds to 50kb; longest gene in 650kb = 24,338bp (TASK data)
maxseg <- 1000 
maxk   <- 1000
seg    <- segment(array$value, maxk=maxk, maxseg=maxseg)
seg at x  <-array$Y/2 # add midpoints of probes to the segmentation object

# Do plotAlongChrom
seg at x <- as.vector(1:nrow(seg at y))
seg at flag <- rep(as.integer(0), times=12995)
seg at nrSegments <- as.integer(111)

segObj <- new.env(parent=baseenv())
assign("1.+", seg, segObj)

grid.newpage()
plotAlongChrom(segObj, chr=1, coord=c(1, 100000), gff=gff)

I am finding the documentation in the R help and the "Segmentation demo"
hard to follow and I would be grateful for any help about where I am going
wrong.

Thanks

Krys


Dr Krystyna A Kelly
University of Cambridge
Department of Pathology
Molteno Building, Tennis Court Road
Cambridge CB2 1QP
Tel:    01223 333331
Email: kak28 at cam.ac.uk