Question: UcscTrack scan() error
0
gravatar for shuoguo
3.5 years ago by
shuoguo10
shuoguo10 wrote:

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

gviz • 582 views
ADD COMMENTlink modified 3.4 years ago by florian.hahne@novartis.com1.6k • written 3.5 years ago by shuoguo10
Answer: UcscTrack scan() error
0
gravatar for florian.hahne@novartis.com
3.4 years ago by
Switzerland

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

ADD COMMENTlink written 3.4 years ago by florian.hahne@novartis.com1.6k

Thanks! Will do.

- Shuoguo

ADD REPLYlink written 3.1 years ago by shuoguo10

Hi Shuoguo,

Did you ever get a solution for this? I ran into the same issue.

Thanks!

ADD REPLYlink written 2.7 years ago by cardenasca40
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