L8-LD-score

R package build

2021-02-18

Tags: example hgen471-2020

LD score

suppressMessages(library(tidyverse))
work.dir ="~/Downloads/ldscore/"

ld score regression

## read ld-score in chr 22 calculated by Yanyu Liang using the GTEx V8 SNP set
ldscore = read.table(paste0(work.dir,"chr22.l2.ldscore.gz"),header=T,as.is=T)
head(ldscore)
## plot ldscore to get a sense of variability
hist(ldscore$L2,xlab="LD Score" , main ="Histogram of LD score")
plot(ldscore$BP, ldscore$L2,xlab="Chr 22 Position",ylab="LD Score", main = "LD Score across chr 22")
ind = 1:5000; ind = ind + 10000;plot(ldscore$BP[ind], ldscore$L2[ind],xlab="Chr 22 Position",ylab="LD Score")
## read GWAS result for height from the GIANT consortium (chr22 only)
giant = read.table(paste0(work.dir,"gwas_giant_chr22.txt"),header=T, as.is=T)
names(giant) = c("variant_id",      "panel_variant_id",        "chromosome",      "position",        "effect_allele",   "non_effect_allele",       "frequency",       "pvalue",  "zscore",  "effect_size",     "standard_error",  "sample_size",     "n_cases")
tempo = inner_join(giant,ldscore,by=c("panel_variant_id"="SNP") )
## plot Chi2 vs LD score
plot(tempo$zscore^2~ tempo$L2)
ggplot(tempo, aes(L2, zscore^2)) + geom_point(alpha=0.5,size=3) +geom_smooth(method="lm") 
fit = lm(tempo$zscore^2~ tempo$L2)
summary(fit)

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Text and figures are licensed under Creative Commons Attribution CC BY 4.0. The source code is licensed under MIT.

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Citation

For attribution, please cite this work as

R package build (2021). L8-LD-score. BIOS 25328 Cancer Genomics Class Notes. /post/2021/02/18/l8-ld-score/

BibTeX citation

@misc{
  title = "L8-LD-score",
  author = "R package build",
  year = "2021",
  journal = "BIOS 25328 Cancer Genomics Class Notes",
  note = "/post/2021/02/18/l8-ld-score/"
}