vague message in gene ID conversion

[katehoffshutta]

The message There was at least one one-to-many mapping (most probably from multiple ensembl IDs for the input) is output from the geneENSGToName function, but the output suggests this is a many-to-one mapping, and the lack of inclusion of the original ENSG in the output table makes it hard to understand.

Changes to be made:

1. the original ENSG should be returned as part of the output table
2. the informational message should be clarified (is it many-to-one or one-to-many?), and probably set as a warning

Example of such output is given below.

> expr_gene_map %>% dplyr::filter(gene_id_no_ver %in% gene_id_no_ver[duplicated(gene_id_no_ver)])
    gene_id_no_ver     gene_name
1  ENSG00000169093         ASMTL
2  ENSG00000169093         ASMTL
3  ENSG00000205755         CRLF2
4  ENSG00000205755         CRLF2
5  ENSG00000223571     DHRSX-IT1
6  ENSG00000223571     DHRSX-IT1
7  ENSG00000237040        DPH3P2
8  ENSG00000237040        DPH3P2
9  ENSG00000178605        GTPBP6
10 ENSG00000178605        GTPBP6
11 ENSG00000229232      KRT18P53
12 ENSG00000229232      KRT18P53
13 ENSG00000230542     LINC00102
14 ENSG00000230542     LINC00102
15 ENSG00000226179     LINC00685
16 ENSG00000226179     LINC00685
17 ENSG00000265658       MIR3690
18 ENSG00000265658       MIR3690
19 ENSG00000277120       MIR6089
20 ENSG00000277120       MIR6089
21 ENSG00000223274     RNA5SP498
22 ENSG00000223274     RNA5SP498
23 ENSG00000223511 RP13-297E16.4
24 ENSG00000223511 RP13-297E16.4
25 ENSG00000225661       RPL14P5
26 ENSG00000225661       RPL14P5
27 ENSG00000169100       SLC25A6
28 ENSG00000169100       SLC25A6
29 ENSG00000223484        TRPC6P
30 ENSG00000223484        TRPC6P

[pmandros]

The geneENSGToName does not return "There was at least one one-to-many ..." because Ensembl IDs get mapped to unique names/symbols such as HUGO. Most probably you are referring to the conversion functions that map to Ensembl IDs (e.g., geneEntrezToENSG), where it can happen that one name gets mapped to multiple Ensembl IDs (one-to-many). For these cases the message "There was at least one one-to-many ..." acts as a warning and the table returned contains all such cases. See example below. I am closing this issue.

> my_friend = NetworkDataCompanion::CreateNetworkDataCompanionObject()
> gene_entrez_list = c(4282,7157,7473)
> my_friend$geneEntrezToENSG(gene_entrez)
[1] "There was at least one one-to-many mapping (most probably from multiple ensembl IDs for the input)"
      gene_entrez  gene_id_no_ver
24659        4282 ENSG00000240972
24660        4282 ENSG00000276701
58814        7157 ENSG00000141510
61484        7473 ENSG00000277626
61485        7473 ENSG00000108379
61486        7473 ENSG00000277641

[katehoffshutta]

Thanks @pmandros! I see what you are describing above, and it makes sense to me, but I do actually see this issue with geneENSGToName. Try this MWE:

my_friend = NetworkDataCompanion::CreateNetworkDataCompanionObject()
my_friend$geneENSGToName(c("ASMTL"))
[1] "There was at least one one-to-many mapping (most probably from multiple ensembl IDs for the input)"
      gene_id_no_ver gene_name
4907 ENSG00000169093     ASMTL
4908 ENSG00000169093     ASMTL

The reason for this appears to be related to genes appearing on both chrX and chrY, I am guessing related to the PAR:

library(dplyr)
my_friend$gene_mapping %>% dplyr::filter(gene_name == "ASMTL")
  seqid source type   start     end score strand phase            gene_id
1  chrX HAVANA gene 1403139 1453762    NA      -    NA ENSG00000169093.15
2  chrY HAVANA gene 1403139 1453762    NA      -    NA ENSG00000169093.15
  gene_name gene_entrez      gene_type  gene_id_no_ver
1     ASMTL        8623 protein_coding ENSG00000169093
2     ASMTL        8623 protein_coding ENSG00000169093

I'm working on resolving this and so have reopened the issue.

Note the item (1) above, "the original ENSG should be returned as part of the output table" is encompassed by #41 and will be addressed there.