LDSC_enrichment
Last updated: 2021-09-01
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Knit directory: funcFinemapping/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 4db9eb3 | Jing Gu | 2021-09-01 | compute standardized effect sizes |
| html | 05f73e9 | Jing Gu | 2021-09-01 | Build site. |
| Rmd | bed838e | Jing Gu | 2021-09-01 | update evaluations on slicing |
Partitioned-LDSC
Technical details
HapMap3 SNPs (~1.2M): used as a proxy for well imputed SNPs and the regression SNPs in LDSC. They were generated by the international HapMap project on a collection of 1301 samples from a variaty of human populations.[https://www.sanger.ac.uk/resources/downloads/human/hapmap3.html]
Reference panel SNPs (~9M): the set of 1000G SNPs with MAF > 5% in ~500 Euproean samples
LDSC inputs/outputs: * .M/.l2.M_5_50: The .M file contains the total number of SNPs; the .l2.M_5_50 file contains the number of SNPs with minor allele frequency above 5%. By default, ldsc uses common SNPs (MAF > 5%) to estimate per SNP heritability, which is different for rare variants.
- freqfile/w-ld-chr: computed on European of Phase 3 of 1kg Genomes
Regression weights: used to correct for non-independence and heteroskedasticity among the \(\chi^2\) statistics.
Regression coefficients: Quoted from the website that "They measure the additional contribution of one annotation to the model and are interpretable for both binary and continuous annotations"
GC correction:
Baseline annotations:
DHS, H3K4me1, H3K4me3, and H3K9ac - peaks w/o flanking regions Coding, Conserved, CTCF, DGF
FANTOM5-Enhancer, Enhancer, Fetal_DHS, H3K27ac
Intron, PromoterFlanking, Promoter, Repressed, Super-enhancer, TFBS, Transcribed TSS
3-prime UTR, 5-prime UTR, Weak Enhancer
Across traits
per-standardized-annotation effect sizes
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| Version | Author | Date |
|---|---|---|
| 05f73e9 | Jing Gu | 2021-09-01 |
Heritability Enrichment across traits and annotations 
sessionInfo()R version 4.0.4 (2021-02-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
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