i am using gviz and it has been awesome. but i could not get the H3K27Ac tracks work properly. it sometimes works:

> htrack <- UcscTrack(genome = "hg19",

+                           chromosome = "chr7",

+                           track = "Layered H3K27Ac",

+                           table = "wgEncodeBroadHistoneGm12878H3k27acStdSig",

+                           from = 148550000,

+                           to = 148560000,

+                           trackType = "DataTrack",

+                           start = "start",

+                           end = "end",

+                           data = "score",

+                           type = "hist",

+                           window = -1,

+                           windowSize = 1500,

+                           fill.histogram = "black",

+                           name = "H3K27Ac")

but when the range is different, it gives error:

htrack2 <- UcscTrack(genome = "hg19",

+                           chromosome = "chr7",

+                           track = "Layered H3K27Ac",

+                           table = "wgEncodeBroadHistoneGm12878H3k27acStdSig",

+                           from = 148550000,

+                           to = 148660000,

+                           trackType = "DataTrack",

+                           start = "start",

+                           end = "end",

+                           data = "score",

+                           type = "hist",

+                           window = -1,

+                           windowSize = 1500,

+                           fill.histogram = "black",

+                           name = "H3K27Ac")

Error in UcscTrack(genome = "hg19", chromosome = "chr7", track = "Layered H3K27Ac",  :

  Error fetching data from UCSC

In addition: Warning message:

In UcscTrack(genome = "hg19", chromosome = "chr7", track = "Layered H3K27Ac",  :

  Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :

  scan() expected 'an integer', got 'section'

Any idea how to get by-passing the error?

thanks,

Shuoguo

This is not a problem with Gviz, but rather with rtracklayer which handles all the communication with UCSC. I'd suggest to set

options(error=recover)

and navigate in the call stack to find the rtracklayer call that fails. With that you can contact the rtracklayer package maintainers for some more help.

Florian