z0on / emapper_to_gomwu_kogmwu Goto Github PK

Thanks for creating the KOGMWU package. Not sure if this is the best venue to post a question, but I'm running into the following error about differing rows when doing a KOGMWU analysis:

kog.mwu(temp, ApalmKOG, Alternative = "t")

Warning: NAs introduced by coercionWarning: cannot xtfrm data frames[1] "Continuous measure of interest: will perform MWU test"
[1] "skipping integer(0) nseqs = 1"
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 1, 0

6. stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), collapse = ", ")), domain = NA)
5. data.frame(..., check.names = FALSE)
4. cbind(deparse.level, ...)
3. cbind(term = as.character(terms), res)
2. kog.mwut(annotated, Alternative)
1. kog.mwu(temp, ApalmKOG, Alternative = "t")

My input files:

data.txt
gene2kog.txt

Is there a reason why I'm getting this error? From my understanding, the two input data frames can have differing rows. Thanks for your help!

Question mostly about KOG_MWU: is there a statistical or biologically-relevant reason to exclude genes with multiple KOG annotations, unlike GO_MWU which allows multiple GO annotations per gene? Is it because there isn't the same kind of hierarchy with KOG?

Hi,

I want to make comparisons between the KOG annotation info from two different species/datasets using KOG_MWU. Each has eggnog annotation data, but I am having trouble extracting the info with the code you provided. Can you elaborate on what your commands are doing (or an example of the end format of the files needed for KOGMWU)?

The annotation information I have was generated with two different versions of eggnog (species 2 output was reformatted with dammit), so I am wondering if I need to re-run so that the output is similar. I am also noticing that in addition to KOG IDs, I am getting COG and ENOG IDs, but I am not sure what these are, or if they can be used?

I have attached an example of the output for each species for reference. I appreciate any help/advice you may have!

Species1.txt
Species2.txt