Question: ENCODE examples from vignette do not work (missing data?)
0
2.4 years ago by
rdmorin0
rdmorin0 wrote:

There seems to be an issue in the current version of coMET. The images are missing from the latest user guide (Compiled: April 24, 2017). This doesn't seem to be a particularly new problem and I suspect it relates to some large data sets that may have been removed from the repository. The issue seems to cause Figure 8 and 9 in the user guide to fail to generate. It looks like the ENCODE data directory and, specifically, the bed file being referenced are missing.

library(coMET)
extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
bedFilePath <- file.path(extdata, "ENCODE/motifs1000_matches_ENCODE.txt")
motif_color <- file.path(extdata, "ENCODE/TFmotifs_colors.csv")
chipTFtrack <- ChIPTF_ENCODE(gen,chr,start, end, bedFilePath,
featureDisplay=c("AHR::ARNT::HIF1A_1",
"AIRE_1","AIRE_2","AHR::ARNT_1"),
motif_color,type_stacking="squish",showId=TRUE)

Error in file(file, "rt") : cannot open the connection
In file(file, "rt") :
cannot open file '/mnt/thanos_lv/rmorin/rmorin/R/x86_64-pc-linux-gnu-library/3.3/coMET/extdata/ENCODE/motifs1000_matches_ENCODE.txt': No such file or directory

Can this be fixed or is there a known workaround?

comet • 345 views
modified 2.0 years ago by Tiphaine Martin40 • written 2.4 years ago by rdmorin0

We have reached out to the coMET maintainer as this is an issue with their package.  We hope they will be responsive soon.

Hi,

Sorry for the delay to answer. The new version of coMET have the file ENCODE data directory.

Regards,

tiphaine

Answer: ENCODE examples from vignette do not work (missing data?)
0
2.0 years ago by
France
Tiphaine Martin40 wrote:

Hi,

Sorry for the delay to answer. The new version of coMET have the file ENCODE data directory.

Regards,

tiphaine