Miscellaneous analysis
This section accommodates many largely independent tasks.
Implementation might well be generic so that both proteins and peptides are covered.
Programs and applications
These are summarised in the following table,
| Program | Description |
|---|---|
csq.sh |
Consequences of variants |
Caprion_deCODE_UKB_PPP.sh |
Caprion/deCODE/UKB-PPP replication |
eSet.sh |
ExpresssionSet implementations |
glmnet_pense.sh |
glmnet/pense modeling |
impute.sb |
imputation experiments |
json.sh |
JSON file generation |
peptideAssociationPlot.sh |
protein Manhattan-peptide signal plots |
dup-pgwas.sh |
pGWAS for duplicated proteins |
dup-extract.sh |
pQTL extractions |
dup-json.sh |
LocusZoom.js plots |
dup-plot.sh |
pQTL plots |
dup-tbl.R |
pQTL table |
pqtlGWAS.R |
pQTL-GWAS lookup |
tables.sh |
Supplementary-Tables.xlsx generator |
ToDo.sh |
various staged experiments |
NB: impute.sb employs impute_parallel() when N(isotope groups) > 500. Nevertheless,
when coming to protein requantification this is an option to use the orginal intensity
data.
Legacy codes
compare.sb. earlier contrast with deCODE/UKB-PPP.inf1.sh. snapshot from SCALLOP/INF meta-analysis.
Created on 20/11/2024