Question: Error: could not find function "readGVF"
0
gravatar for Vinicius Henrique da Silva
4.2 years ago by
Brazil

I am trying to use the 'readGVF' function but it seems to be inexistent.
 

> library("cnvGSAdata")
> library(cnvGSA)
> readGVF()
Error: could not find function "readGVF"
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=C                  LC_COLLATE=C
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] cnvGSAdata_1.6.0      cnvGSA_1.14.0         splitstackshape_1.4.2
 [4] data.table_1.9.6      GenomicRanges_1.22.0  GenomeInfoDb_1.6.0
 [7] IRanges_2.4.0         S4Vectors_0.8.0       BiocGenerics_0.16.0
[10] doParallel_1.0.10     iterators_1.0.8       foreach_1.4.3
[13] brglm_0.5-9           profileModel_0.5-9    BiocInstaller_1.20.0

loaded via a namespace (and not attached):
[1] codetools_0.2-14 chron_2.3-47     zlibbioc_1.16.0  XVector_0.10.0
[5] tools_3.2.2

Any idea why?

cnv gvf cnvgsa • 770 views
ADD COMMENTlink modified 4.2 years ago by James W. MacDonald52k • written 4.2 years ago by Vinicius Henrique da Silva40
Answer: Error: could not find function "readGVF"
0
gravatar for James W. MacDonald
4.2 years ago by
United States
James W. MacDonald52k wrote:

Can you say what package you expect that function to be in? There is no indication that I can see that the function is part of cnvGSA, and a search of the entire BioC subversion using Itoshi Nikaido's awesome search page doesn't come up with that function name in any BioC package.

ADD COMMENTlink written 4.2 years ago by James W. MacDonald52k

I got the function from this website:
http://rgm3.lab.nig.ac.jp/RGM/R_rdfile?f=cnvGSA/man/readGVF.Rd&d=R_BC
Moreover, I found 'readGVF' function in cnvGSA vignette (page6).

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Vinicius Henrique da Silva40
1

Right. And that page shows that they are using R-3.0.2, which is old. The last version of cnvGSA that had that function is three releases ago. If you want to use the version of that package that has that function, you could install R-3.0.2 and then use biocLite() to install. Or you could use the current version - I assume the updated vignette is also updated vis a vis reading in data, so I would start there.

ADD REPLYlink written 4.2 years ago by James W. MacDonald52k
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