chrom_ld: chrom_ld

In dengchunyu/scPagwas: A pathway-based polygenic integration method for inferring disease-associated individual cells in single cell sequencing data

chrom_ld

Description

use vcftools to get ped and map files LD data from /share/apps/vcftools/bin/vcftools --vcf /share/pub/dengcy/Singlecell/COVID19/1000genomes_all_genotypes.vcf --plink-tped --out /share/pub/dengcy/Singlecell/COVID19/1000genomes_all_genotypes /share/pub/dengcy/Singlecell/COVID19/PLINK/plink --tfile /share/pub/dengcy/Singlecell/COVID19/1000genomes_all_genotypes --recode --out /share/pub/dengcy/Singlecell/COVID19/1000genomes_all_genotypes /share/pub/dengcy/Singlecell/COVID19/PLINK/plink --map /share/pub/dengcy/Singlecell/COVID19/1000genomes_all_genotypes.map --ped /share/pub/dengcy/Singlecell/COVID19/1000genomes_all_genotypes.ped --allow-no-sex --autosome --r2 --ld-window-kb 1000 --ld-window-r2 0.2 --out /share/pub/dengcy/Singlecell/COVID19/ld_1000genome covid_ld<-read.delim("/share/pub/dengcy/Singlecell/COVID19/ld_1000genome.ld") covid_ld<-covid_ld[!(covid_ld$ colnames(covid_ld)[7]<-"R" lapply(unique(covid_ld$CHR_A), function(i){ a<-data.table(covid_ld[covid_ld$CHR_A == i,]) file_name <- paste0("/share/pub/dengcy/Singlecell/COVID19/data/LD/",i,".Rds") saveRDS(a, file = file_name) }) chrom_ld<-lapply(as.character(1:22),function(chrom){ chrom_ld_file_path <- paste(ld_folder, '/', chrom, '.Rds', sep = '') ld_data <- readRDS(chrom_ld_file_path)[(R**2 > r2_threshold), .(SNP_A, SNP_B, R)] return(ld_data) }) save(chrom_ld,file="/share/pub/dengcy/GWAS_Multiomics/pagwas/data/chrom_ld.RData")

Usage

data(chrom_ld)

Format

a list.

Source

Generated from PLINK 1.90 linux

Examples

data(chrom_ld)
str(chrom_ld)

dengchunyu/scPagwas documentation built on Nov. 29, 2024, 2:53 p.m.