document rownames
Closed this issue · 4 comments
lwaldron commented
What are the integer row names?
> mae <- scNMT(dry.run = FALSE)
> rownames(mae)
CharacterList of length 13
[["acc_cgi"]] 2886 3126 202 2535 2172 702 ... 1150 3075 1684 3706 460 304
[["acc_CTCF"]] 766 234 188 786 277 480 488 ... 330 243 219 851 201 893
[["acc_DHS"]] 36 30 234 192 230 288 181 284 ... 169 56 97 183 246 244 21
[["acc_genebody"]] 9716 15943 16258 15982 16871 ... 2577 10872 7667 4883
[["acc_p300"]] 85 84 25 78 126 8 9 83 87 ... 105 127 129 101 110 69 40 81
[["acc_promoter"]] 11640 11053 2076 15434 4399 ... 12389 16241 15746 3862
[["met_cgi"]] 2907 5076 5335 5285 2813 5004 ... 3084 4782 2664 2912 2972
[["met_CTCF"]] 124 74 68 32 42 173 21 5 ... 158 78 161 22 110 115 159 36
[["met_DHS"]] 25 13 2 33 22 32 39 12 43 27 ... 1 52 6 42 40 66 54 55 51
[["met_genebody"]] 13829 3869 9078 4461 665 ... 8612 11880 14651 15269LiNk-NY commented
@lwaldron
This looks like strange behavior. I've tried tracing the issue but I'm getting inconsistent results.
I will keep looking into it. The row names should look like ENMUSG0000XXX etc.
lwaldron commented
This is in the waldronlab/bioconductor:devel container if that helps.