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?

Hi,

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

Regards,

tiphaine