Question

Error in classify_gene_pairs

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Entering edit mode

hfyuan2016 • 0

@hfyuan2016-23538

Last seen 8 months ago

Australia

Hi, I am using DoubleTrouble to analyze the duplicate genes in my aim genome.

I met error when I used the classify_gene_pairs function:

> YY.class <- classify_gene_pairs(annotation =YY.pdata$annotation,
+                                 blast_list = YY_diamond,
+                                 scheme = "standard",
+                                 evalue = 1e-10,
+                                 anchors = 5,
+                                 max_gaps = 25,
+                                 proximal_max = 10)
Error in classify_gene_pairs(annotation = YY.pdata$annotation, blast_list = YY_diamond,  : 
  unused argument (scheme = "standard")

Many thanks for help.

syntenet doubletrouble • 475 views

ADD COMMENT • link 8 months ago hfyuan2016 • 0

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Entering edit mode

Hi,

It looks like you're using an old version of doubletrouble, from when the argument scheme did not exist. As James rightly pointed out, showing your session info would help identify the problem. Please, update your version of doubletrouble (and maybe Bioconductor, if you're using an old version of Bioconductor) and see if the error disappears.

Best,

Fabricio

ADD REPLY • link 8 months ago Fabricio Almeida-Silva ▴ 40

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Entering edit mode

Hi Fabricio,

Yes, you are right. I updated my R, BioManager, and doubletrouble. It works now.

Thank you so much.

Have a good day.

Regards, Huifang

ADD REPLY • link 8 months ago hfyuan2016 • 0

score 0 · Answer 1 · 2024-03-11

You need to include the output from running sessionInfo() as well. But it appears to be fine to me.

> library(doubletrouble)
Warning message:
package 'doubletrouble' was built under R version 4.3.2 
> example("classify_gene_pairs")

clss__> # Load example data
clss__> data(diamond_intra)

clss__> data(diamond_inter)

clss__> data(yeast_annot)

clss__> data(yeast_seq)

clss__> # Get processed annotation data
clss__> annotation <- syntenet::process_input(yeast_seq, yeast_annot)$annotation

clss__> # Get list of intron counts
clss__> txdb_list <- lapply(yeast_annot, GenomicFeatures::makeTxDbFromGRanges)

clss__> intron_counts <- lapply(txdb_list, get_intron_counts)

clss__> # Classify duplicates - full scheme
clss__> dup_class <- classify_gene_pairs(
clss__+     annotation = annotation, 
clss__+     blast_list = diamond_intra, 
clss__+     scheme = "full",
clss__+     blast_inter = diamond_inter, 
clss__+     intron_counts = intron_counts
clss__+ )

clss__> # Check number of gene pairs per class
clss__> table(dup_class$Scerevisiae$type)

  SD   TD   PD rTRD dTRD   DD 
 342   42   80   52  963 2109 

> dup_class <- classify_gene_pairs(
         annotation = annotation, 
         blast_list = diamond_intra, scheme = "standard",blast_inter = diamond_inter, 
         intron_counts = intron_counts
     )


> head(dup_class[[1]])
           dup1        dup2 type
124 Sce_YGR032W Sce_YLR342W   SD
176 Sce_YOR396W Sce_YPL283C   SD
189 Sce_YJL225C Sce_YIL177C   SD
275 Sce_YNR031C Sce_YCR073C   SD
285 Sce_YOR326W Sce_YAL029C   SD
312 Sce_YJL222W Sce_YIL173W   SD

And

> sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22621)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] doubletrouble_1.2.5 BiocManager_1.30.22