Epigenomewide association
jinghuazhao edited this page Jun 3, 2018
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This is furnished with ewas.sh and ewas.subs, along with a few other files as follows,
| Files | Description |
|---|---|
| ewas.sh | EWAS imputation |
| ewas.subs | subroutine called by ewas.sh |
| get_weight.qsub | SGE script for EWAS weight generation |
| get_weight_subs | subroutine callable from get_weight.qsub and parallel
|
| CpG.lst | list of probe IDs with weights |
| weights/ | directory containing weights for all probes as specfied in CpG.lst
|
| EWAS/ | directory containing PLINK binary files for each probe |
| EWAS.pheno |
PLINK phenotype file with header for all probes |
| EWAS.bim |
PLINK .bim file sorted by SNP IDs |
This implementation used the same idea as TWAS. Data from 1000Genomes imputation were scaled down to those
in HapMap II to make the weight generation more tenable to sample size. Note that weights were obtained
for all probes so it is possible to impute for only subset(s) of them. The file EWAS.bim was generated
in order to make it easier to align strands for SNPs as in GWAS with those in the reference panel.
Additional information is now available from EWAS-fusion.