KOGMWU error about differing rows about emapper_to_gomwu_kogmwu

[z0on]

Hi - thanks for giving my package a shot! The data files look fine, but are you sure they are imported correctly into R? I mean, I would check that my input datasets (temp and ApalmKOG) look like nice healthy data frames in R.

On Mon, Mar 6, 2023 at 2:08 PM Dr. Yaamini R. Venkataraman < ***@***.***> wrote: 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 <https://github.com/z0on/emapper_to_GOMWU_KOGMWU/files/10902367/data.txt> gene2kog.txt <https://github.com/z0on/emapper_to_GOMWU_KOGMWU/files/10902368/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! — Reply to this email directly, view it on GitHub <#3>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZUHGGLVNKMXUN5INA622LW2Y72HANCNFSM6AAAAAAVRSJK5M> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- cheers Misha matzlab.weebly.com

[yaaminiv]

Hi Misha,

The data frames look fine in R. I modeled them after the larval and adult data included with the KOGMWU package with gene and KOG data as factors.

> str(temp)
tibble [400 × 2] (S3: tbl_df/tbl/data.frame)
 $ ApalmGeneID: Factor w/ 400 levels "evm.model.hic_scaffold_1.11",..: 1 2 3 4 5 6 7 8 9 10 ...
 $ log2fc     : num [1:400] 0.484 0.999 -0.977 -0.943 0.832 ...

>head(temp)
# A tibble: 6 × 2
  ApalmGeneID                   log2fc
  <fct>                          <dbl>
1 evm.model.hic_scaffold_1.11    0.484
2 evm.model.hic_scaffold_1.1206  0.999
3 evm.model.hic_scaffold_1.1237 -0.977
4 evm.model.hic_scaffold_1.1322 -0.943
5 evm.model.hic_scaffold_1.1436  0.832
6 evm.model.hic_scaffold_1.1476  0.440

> str(ApalmKOG)
tibble [11,697 × 2] (S3: tbl_df/tbl/data.frame)
 $ ApalmGeneID: Factor w/ 10362 levels "evm.model.hic_scaffold_1.1",..: 1 1 2 3 4 5 6 7 8 9 ...
 $ KOG        : Factor w/ 23 levels "Amino acid transport and metabolism",..: 22 17 18 18 8 21 18 21 21 21 ...

> head(ApalmKOG)
# A tibble: 6 × 2
  ApalmGeneID                             KOG                                                         
  <fct>                                   <fct>                                                       
1 evm.model.hic_scaffold_1.1              Transcription                                               
2 evm.model.hic_scaffold_1.1              Posttranslational modification, protein turnover, chaperones
3 evm.model.hic_scaffold_1.101            Replication, recombination and repair                       
4 evm.model.hic_scaffold_1.101.1.5f5b2bfd Replication, recombination and repair                       
5 evm.model.hic_scaffold_1.1013           Cytoskeleton                                                
6 evm.model.hic_scaffold_1.102            Signal transduction mechanisms  

I'm don't see any problems outright, so I'd appreciate any insight you have!

[yaaminiv]

Hi @z0on I'm still getting errors when I try to run KOGMWU:

> kog.mwu(data = temp, gene2kog = ApalmKOG, Alternative = "t")

Error in xtfrm.data.frame(x) : cannot xtfrm data frames
11. stop("cannot xtfrm data frames")
10. xtfrm.data.frame(x)
9. | xtfrm(x)
8. as.vector(xtfrm(x))
7. FUN(X[[i]], ...)
6. lapply(z, function(x) if (is.object(x)) as.vector(xtfrm(x)) else x)
5. order(y)
4. factor(x)
3. as.factor(annotated[, 2])
2. levels(as.factor(annotated[, 2]))
1. kog.mwu(data = temp, gene2kog = ApalmKOG, Alternative = "t")

Any suggestions for how to get around this?

[z0on]

Apologies for radio silence, this somehow fell behind my event horizon - this looks strange… These objects are not supposed to be tibbles, they must be simple data frames. Can you send your whole code with all input files?

…

On Nov 8, 2023, at 1:35 PM, Dr. Yaamini R. Venkataraman ***@***.***> wrote: Hi @z0on <https://github.com/z0on> I'm still getting errors when I try to run KOGMWU: > kog.mwu(data = temp, gene2kog = ApalmKOG, Alternative = "t") Error in xtfrm.data.frame(x) : cannot xtfrm data frames 11. stop("cannot xtfrm data frames") 10. xtfrm.data.frame(x) 9. | xtfrm(x) 8. as.vector(xtfrm(x)) 7. FUN(X[[i]], ...) 6. lapply(z, function(x) if (is.object(x)) as.vector(xtfrm(x)) else x) 5. order(y) 4. factor(x) 3. as.factor(annotated[, 2]) 2. levels(as.factor(annotated[, 2])) 1. kog.mwu(data = temp, gene2kog = ApalmKOG, Alternative = "t") Any suggestions for how to get around this? — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABZUHGATRGTGFUTQDKJNUOLYDPNHPAVCNFSM6AAAAAAVRSJK5OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMBSGUZDSMBQHE>. You are receiving this because you were mentioned.

[yaaminiv]

Converting my tibbles to data frames with as.data.frame allowed me to run my data through KOGMWU! Thanks for pointing that out