read_homer_output not reading files

[lavkan]

I am passing the path to the folder from the current working directory and the command "read_homer_output()" is not reading any motif tsv files, although there are such files. Should the folder name with paths should be passed differently?

h <- read_homer_output("Question2_Homer/q2_group1_translated_genes_MPvsLSK-f7vstot_both_up_g")
h
list()
names(h)
NULL
list.files("Question2_Homer/q2_group1_translated_genes_MPvsLSK-f7vstot_both_up_g/homerResults/", pattern = ".motif")
[1] "motif1.motif" "motif1.motif.tsv" "motif10.motif" "motif10.motif.tsv"
[5] "motif10.similar1.motif" "motif10.similar1.motif.tsv" "motif10RV.motif" "motif10RV.motif.tsv"
[9] "motif11.motif" "motif11.motif.tsv" "motif11RV.motif" "motif11RV.motif.tsv"
[13] "motif12.motif" "motif12.motif.tsv" "motif12RV.motif" "motif12RV.motif.tsv"
[17] "motif13.motif" "motif13.motif.tsv" "motif13RV.motif" "motif13RV.motif.tsv"
[21] "motif14.motif" "motif14.motif.tsv" "motif14RV.motif" "motif14RV.motif.tsv"
[25] "motif15.motif" "motif15.motif.tsv" "motif15RV.motif" "motif15RV.motif.tsv"
[29] "motif1RV.motif" "motif1RV.motif.tsv" "motif2.motif" "motif2.motif.tsv"
[33] "motif2RV.motif" "motif2RV.motif.tsv" "motif3.motif" "motif3.motif.tsv"
[37] "motif3.similar1.motif" "motif3.similar1.motif.tsv" "motif3RV.motif" "motif3RV.motif.tsv"
[41] "motif4.motif" "motif4.motif.tsv" "motif4RV.motif" "motif4RV.motif.tsv"
[45] "motif5.motif" "motif5.motif.tsv" "motif5RV.motif" "motif5RV.motif.tsv"
[49] "motif6.motif" "motif6.motif.tsv" "motif6.similar1.motif" "motif6.similar1.motif.tsv"
[53] "motif6RV.motif" "motif6RV.motif.tsv" "motif7.motif" "motif7.motif.tsv"
[57] "motif7RV.motif" "motif7RV.motif.tsv" "motif8.motif" "motif8.motif.tsv"
[61] "motif8RV.motif" "motif8RV.motif.tsv" "motif9.motif" "motif9.motif.tsv"
[65] "motif9RV.motif" "motif9RV.motif.tsv"

[slowkow]

Sorry for the issue! I haven't developed this package much. It was useful for one of my big HOMER runs and I probably did not anticipate different folder structures.

You can see how my folders were arranged by reading the code:

  novel_motif_files <- Sys.glob(
    paths = c(
      file.path(folder, "homerResults", "motif*.motif.tsv"),
      file.path(folder, "homerResults", "motif*.motif.tsv.gz")
    )
  )

https://github.com/slowkow/homerkit/blob/master/R/read_homer_output.R#L10-L15

I hope that helps. Please feel free to copy my code and change it, or submit a pull request if you want to improve it!