ENCODE examples from vignette do not work (missing data?)
1
0
Entering edit mode
rdmorin • 0
@rdmorin-13400
Last seen 6.7 years ago

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 addition: Warning message:
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 • 958 views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Hi,

 

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

Regards,

tiphaine

ADD REPLY
0
Entering edit mode
@tiphaine-martin-6416
Last seen 5.5 years ago
France

Hi,

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

Regards,

tiphaine

ADD COMMENT

Login before adding your answer.

Traffic: 616 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6