Closed runjin326 closed 3 years ago
@runjin326 can you merge the PMTL updates for the ensg-hugo-pmtl-mapping.tsv
module and the long-format-table-utils
module that will enable me to update the dependent modules that you have listed in the ticket?
@ewafula, it is already merged :) I mentioned in the ticket. You should be able to get it once you do a dev pull and merge.
@ewafula, it is already merged :) I mentioned in the ticket. You should be able to get it once you do a dev pull and merge.
@runjin326 The ensg-hugo-pmtl-mapping.tsv
is part of the other PR that is pending final review and merge. When @afarrel or @chinwallaa have reviewed it, I will reach out to you to merge it.
@runjin326, @logstar,
I am encountering assertion errors when running rna-seq-expression-summary-stats
module with the updated ensg-hugo-pmtl-mapping.tsv
mapping file. There is likely a conflict with gene symbols presence between the new PMTL file and expression matrix. What would you recommend we do to address this issue?
Error in get_output_ss_df(x, gsb_gid_df) :
all(rownames(ss_df) %in% rownames(gsb_gids_conv_df)) is not TRUE
Calls: get_expression_summary_stats_out_dfs -> lapply -> FUN -> get_output_ss_df -> stopifnot
Execution halted
Error in get_output_ss_df(x, gsb_gid_df) :
all(rownames(ss_df) %in% rownames(gsb_gids_conv_df)) is not TRUE
Calls: get_expression_summary_stats_out_dfs -> lapply -> FUN -> get_output_ss_df -> stopifnot
Execution halted
Here are new new gene symbols in ensg-hugo-pmtl-mapping.tsv
table absent in ensg-hugo-rmtl-mapping.tsv
table:
ensg_id gene_symbol pmtl version
ENSG00000198793 mTOR Relevant Molecular Target PMTL version 1.1
ENSG00000007312 CD79b Relevant Molecular Target PMTL version 1.1
Symbol_Not_Found GD2 (Disialoganglioside) Relevant Molecular Target PMTL version 1.1
Symbol_Not_Found DNA (alkylators) Relevant Molecular Target PMTL version 1.1
@sangeetashukla, you could delete the first two(mTOR
and CD79b
) because there are just variants of MTOR
and CD79B
already in both tables. Not sure about the last two (GD2
and DNA
) which are more than symbols and don't have corresponding ENSG IDs
Cc @afarrel , @chinwallaa
@runjin326, @logstar, I am encountering assertion errors when running
rna-seq-expression-summary-stats
module with the updatedensg-hugo-pmtl-mapping.tsv
mapping file. There is likely a conflict with gene symbols presence between the new PMTL file and expression matrix. What would you recommend we do to address this issue?Error in get_output_ss_df(x, gsb_gid_df) : all(rownames(ss_df) %in% rownames(gsb_gids_conv_df)) is not TRUE Calls: get_expression_summary_stats_out_dfs -> lapply -> FUN -> get_output_ss_df -> stopifnot Execution halted
Error in get_output_ss_df(x, gsb_gid_df) : all(rownames(ss_df) %in% rownames(gsb_gids_conv_df)) is not TRUE Calls: get_expression_summary_stats_out_dfs -> lapply -> FUN -> get_output_ss_df -> stopifnot Execution halted
Here are new new gene symbols in
ensg-hugo-pmtl-mapping.tsv
table absent inensg-hugo-rmtl-mapping.tsv
table:ensg_id gene_symbol pmtl version ENSG00000198793 mTOR Relevant Molecular Target PMTL version 1.1 ENSG00000007312 CD79b Relevant Molecular Target PMTL version 1.1 Symbol_Not_Found GD2 (Disialoganglioside) Relevant Molecular Target PMTL version 1.1 Symbol_Not_Found DNA (alkylators) Relevant Molecular Target PMTL version 1.1
@sangeetashukla, you could delete the first two(
mTOR
andCD79b
) because there are just variants ofMTOR
andCD79B
already in both tables. Not sure about the last two (GD2
andDNA
) which are more than symbols and don't have correspondingENSG IDs
Cc @afarrel , @chinwallaa
@ewafula My previous PR is now closed and since I encountered errors reading some files directly from S3 bucket, @runjin326 created this PR, and when that is merged you can use a new ensg-hugo-pmtl-mapping.tsv
.
cc @afarrel @chinwallaa
@runjin326, @logstar, I am encountering assertion errors when running
rna-seq-expression-summary-stats
module with the updatedensg-hugo-pmtl-mapping.tsv
mapping file. There is likely a conflict with gene symbols presence between the new PMTL file and expression matrix. What would you recommend we do to address this issue?Error in get_output_ss_df(x, gsb_gid_df) : all(rownames(ss_df) %in% rownames(gsb_gids_conv_df)) is not TRUE Calls: get_expression_summary_stats_out_dfs -> lapply -> FUN -> get_output_ss_df -> stopifnot Execution halted
Error in get_output_ss_df(x, gsb_gid_df) : all(rownames(ss_df) %in% rownames(gsb_gids_conv_df)) is not TRUE Calls: get_expression_summary_stats_out_dfs -> lapply -> FUN -> get_output_ss_df -> stopifnot Execution halted
Here are new new gene symbols in
ensg-hugo-pmtl-mapping.tsv
table absent inensg-hugo-rmtl-mapping.tsv
table:ensg_id gene_symbol pmtl version ENSG00000198793 mTOR Relevant Molecular Target PMTL version 1.1 ENSG00000007312 CD79b Relevant Molecular Target PMTL version 1.1 Symbol_Not_Found GD2 (Disialoganglioside) Relevant Molecular Target PMTL version 1.1 Symbol_Not_Found DNA (alkylators) Relevant Molecular Target PMTL version 1.1
@sangeetashukla, you could delete the first two(
mTOR
andCD79b
) because there are just variants ofMTOR
andCD79B
already in both tables. Not sure about the last two (GD2
andDNA
) which are more than symbols and don't have correspondingENSG IDs
Cc @afarrel , @chinwallaa@ewafula My previous PR is now closed and since I encountered errors reading some files directly from S3 bucket, @runjin326 created this PR, and when that is merged you can use a new
ensg-hugo-pmtl-mapping.tsv
. cc @afarrel @chinwallaa
@sangeetashukla, thank you!
What analysis module should be updated and why?
Since the PR with changes from RMTL to PMTL is in, we now need to change the modules that directly call this file (or use the module
long-format-table-utils
):cnv-frequencies
snv-frequencies
fusion-frequencies
rna-seq-expression-summary-stats
What changes need to be made? Please provide enough detail for another participant to make the update.
For all the above nodules, do the following
ensg-hugo-rmtl-mapping.tsv
- renameensg-hugo-rmtl-mapping.tsv
toensg-hugo-pmtl-mapping.tsv
(currently I see infusion-frequencies
andrna-seq-expression-summary-stats
, but please confirm)What input data should be used? Which data were used in the version being updated?
v9 /v10 Either re-run now and merge or re-run with changes after v10 is released.
When do you expect the revised analysis will be completed?
1-2 days.
Who will complete the updated analysis?
@ewafula