Hello everybody,
I want to explore my data in ChromoViz package, but i have some
difficulties in performing the cViz command. I get an error telling me
that my data object must me atomic, but is.atmoic insists that the
object is indeed atmoic. Yourdata is the example data on the homepage
of
ChromoViz and read into R as a tab file
library(RSvgDevice)
library(XML)
library(ChromoViz)
data(cytoBand9606)
yourdata<-read.table("Result.txt")
cViz(yourdata, cytoBand9606)
#Error in sort(unique.default(x), na.last = TRUE) :
# `x' must be atomic
is.atomic(yourdata)
# [1] FALSE
yourdata2<-as.matrix(yourdata)
is.atomic(yourdata2)
# [1] TRUE
cViz(yourdata2, cytoBand9606)
#Error in sort(unique.default(x), na.last = TRUE) :
# `x' must be atomic
What is this error trying to tell me? Any help is highly appriciated
regards
morten
Im sorry... I figured out this myself.. I was missing the headers in
the
input file. The error has nothing to do with format of the input
object. Maybe an idea to add a check for this in the code?
before:
default 9606 chr7 + 133614711 133628469 4.3
NM_020299
default 9606 chr7 + 39696888 39841925 5.5
NM_003718
after:
track taxonomy chrom strand begin end value item
default 9606 chr7 + 133614711 133628469 4.3
NM_020299
default 9606 chr7 + 39696888 39841925 5.5
NM_003718
morten
> Hello everybody,
>
> I want to explore my data in ChromoViz package, but i have some
> difficulties in performing the cViz command. I get an error telling
me
> that my data object must me atomic, but is.atmoic insists that the
> object is indeed atmoic. Yourdata is the example data on the
homepage
> of ChromoViz and read into R as a tab file
>
>
> library(RSvgDevice)
> library(XML)
> library(ChromoViz)
> data(cytoBand9606)
> yourdata<-read.table("Result.txt")
> cViz(yourdata, cytoBand9606)
> #Error in sort(unique.default(x), na.last = TRUE) :
> # `x' must be atomic
> is.atomic(yourdata)
> # [1] FALSE
> yourdata2<-as.matrix(yourdata)
> is.atomic(yourdata2)
> # [1] TRUE
> cViz(yourdata2, cytoBand9606)
> #Error in sort(unique.default(x), na.last = TRUE) :
> # `x' must be atomic
>
> What is this error trying to tell me? Any help is highly appriciated
>
> regards
> morten
