Update filter-mtp-tables module to utilize targets and disease mapping files from the mtp-annotations module
What changes need to be made? Please provide enough detail for another participant to make the update.
0). Update 01-filter-mtp-tables-for-current-gencode.Rmd script
1). Utilize analyses/mtp-annotations/results/mtp-targets-mapping.tsv.gz and analyses/mtp-annotations/run-mtp-annotations.sh to filter Ensembl IDs and update EFO/MONDO respectively in MTP tables.
2). Include MTP gene-level and isoform-level methylation summary tables from the methylation-summary module
3). Inlcude upcoming DESeq long table
4). Remove 02-filter-mtp-tables-misc-updates.R script - no longer needed from v12 onwards
5). Exclude input/MTP_v11_InvalidENSG_20220831.txt - no longer needed from v12 onwards
What input data should be used? Which data were used in the version being updated?
MTP tables described in the filter-mtp-tables and methylation summary tables
When do you expect the revised analysis will be completed?
jharenza
commented
1 year ago
What analysis module should be updated and why?
Update filter-mtp-tables module to utilize targets and disease mapping files from the
mtp-annotationsmoduleWhat changes need to be made? Please provide enough detail for another participant to make the update.
0). Update
01-filter-mtp-tables-for-current-gencode.Rmdscript 1). Utilizeanalyses/mtp-annotations/results/mtp-targets-mapping.tsv.gzandanalyses/mtp-annotations/run-mtp-annotations.shto filterEnsembl IDsand updateEFO/MONDOrespectively in MTP tables.2). Include MTP gene-level and isoform-level methylation summary tables from the methylation-summary module 3). Inlcude upcoming DESeq long table 4). Remove
02-filter-mtp-tables-misc-updates.Rscript - no longer needed from v12 onwards 5). Excludeinput/MTP_v11_InvalidENSG_20220831.txt- no longer needed from v12 onwardsWhat input data should be used? Which data were used in the version being updated?
MTP tables described in the filter-mtp-tables and methylation summary tables
When do you expect the revised analysis will be completed?
This sprint
Who will complete the updated analysis?
@atlas4213