Last updated: 2020-09-21
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atac = readRDS('/Users/nicholeyang/Desktop/Rotation2/data/interrogation_of_hematicells_data/peakGeneCorrelation.rds')
## load SNPs
load('/Users/nicholeyang/Desktop/Rotation2/gene-level fine mapping/data/snp_hg19_hg38.RData')unique(atac$chr) [1] chrX chr20 chr1 chr6 chr7 chr12 chr4 chr17 chr16 chr2 chr3 chr8
[13] chr19 chr9 chr11 chr13 chr14 chr5 chr10 chr22 chr18 chr15 chr21
23 Levels: chrX chr20 chr1 chr6 chr7 chr12 chr4 chr17 chr16 chr2 chr3 ... chr21length(unique(atac$gene))[1] 11905range(atac$correlation)[1] 0.441 0.989head(atac) chr start end gene correlation p-value
6 chrX 99616179 99616679 TSPAN6 0.448 8.31e-03
16 chrX 99665839 99666339 TSPAN6 0.660 2.78e-06
17 chrX 99666697 99667197 TSPAN6 0.570 1.73e-04
18 chrX 99668153 99668653 TSPAN6 0.572 1.56e-04
21 chrX 99702599 99703099 TSPAN6 0.508 1.52e-03
36 chrX 99890747 99891247 TSPAN6 0.478 3.75e-0399883795 99891794
head(dat_snp) chr start loc_38map
1 chr1 100643730 chr1:100178174-100178174
2 chr1 101361178 chr1:100895622-100895622
3 chr1 10271688 chr1:10211630-10211630
4 chr1 104097685 chr1:103555063-103555063
5 chr1 108588372 chr1:108045750-108045750
6 chr1 108742123 chr1:108199501-108199501unique(dat_snp$chr) [1] chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr2
[13] chr20 chr21 chr22 chr3 chr4 chr5 chr6 chr7 chr8 chr9
22 Levels: chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 ... chr9str(atac)'data.frame': 643072 obs. of 6 variables:
$ chr : Factor w/ 23 levels "chrX","chr20",..: 1 1 1 1 1 1 1 1 1 1 ...
$ start : int 99616179 99665839 99666697 99668153 99702599 99890747 99891545 99983250 99990833 99998134 ...
$ end : int 99616679 99666339 99667197 99668653 99703099 99891247 99892045 99983750 99991333 99998634 ...
$ gene : Factor w/ 12003 levels "TSPAN6","DPM1",..: 1 1 1 1 1 1 1 1 1 1 ...
$ correlation: num 0.448 0.66 0.57 0.572 0.508 0.478 0.631 0.445 0.472 0.52 ...
$ p-value : num 8.31e-03 2.78e-06 1.73e-04 1.56e-04 1.52e-03 3.75e-03 1.18e-05 9.06e-03 4.40e-03 1.04e-03 ...str(dat_snp)'data.frame': 5053 obs. of 3 variables:
$ chr : Factor w/ 22 levels "chr1","chr10",..: 1 1 1 1 1 1 1 1 1 1 ...
$ start : Factor w/ 4875 levels "100000545","100001077",..: 19 44 109 144 235 241 244 254 256 257 ...
$ loc_38map: Factor w/ 4875 levels "chr1:100178174-100178174",..: 1 2 3 4 5 6 7 8 9 10 ...dat_snp$start = as.numeric(as.character(dat_snp$start))
dat_snp$loc_38map = as.character(dat_snp$loc_38map)load('/Users/nicholeyang/Desktop/gene_level_fine_mapping/data/train_add_hic.RData')## map eqtls with atac signature
snp_list = c()
index_list = c()
for (i in 1: dim(dat_snp)[1]){
index = which(as.character(atac$chr) == as.character(dat_snp$chr[i]) & (atac$start < dat_snp$start[i]) & (atac$end > dat_snp$start[i]))
index_list = c(index_list, index)
snp = rep(dat_snp$loc_38map[i], length(index))
snp_list = c(snp_list, snp)
}snp_loc38 = unlist(lapply(strsplit(as.character(snp_list), '-'), function(x) x[1]))
eqtl_atac = cbind(snp_loc38, atac[index_list, ])
colnames(eqtl_atac)[5] = 'gene_name'dat_add_hic_atac = merge(dat_add_hic, eqtl_atac, by = c('gene_name', 'snp_loc38'), all.x = TRUE)
dat_add_hic_atac2 = dat_add_hic_atac[!duplicated(dat_add_hic_atac), ]train_all_sig = dat_add_hic_atac2[,!(names(dat_add_hic_atac2) %in% c('chr', "start","end", 'p-value'))]
train_all_sig[is.na(train_all_sig)] <- 0
save(train_all_sig, file = '/Users/nicholeyang/Desktop/gene_level_fine_mapping/data/train_all.RData')
sessionInfo()R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.5
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] workflowr_1.6.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.4 rprojroot_1.3-2 digest_0.6.25 later_1.0.0
[5] R6_2.4.1 backports_1.1.5 git2r_0.26.1 magrittr_1.5
[9] evaluate_0.14 highr_0.8 stringi_1.4.6 rlang_0.4.5
[13] fs_1.3.2 promises_1.1.0 whisker_0.4 rmarkdown_2.1
[17] tools_3.6.3 stringr_1.4.0 glue_1.3.2 httpuv_1.5.2
[21] xfun_0.12 yaml_2.2.1 compiler_3.6.3 htmltools_0.4.0
[25] knitr_1.28