Zepeng (Phoenix) Mu Zepeng-Mu
🖥️
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ggColocManhattanSingle <- function( | |
| summ.1, chr = "CHR", bp = "BP", p = "P", snp = "SNP", | |
| summ.1.name = expression(paste("", -log[10](P))), | |
| logp = TRUE, size = 2, lead.snp = NULL, r2 = NULL, ... | |
| ) { | |
| if (!is.null(summ.1[[snp]])) { | |
| d1 <- data.frame(CHR = summ.1[[chr]], BP = summ.1[[bp]], P = summ.1[[p]], SNP = summ.1[[snp]]) | |
| } else { | |
| d1 <- data.frame(CHR = summ.1[[chr]], BP = summ.1[[bp]], P = summ.1[[p]]) |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ## Run GLIMPSE on scATAC bam files | |
| import pandas as pd | |
| import os | |
| smp = os.listdir("/project/yangili1/zpmu/covid19/data/cellranger_out21") | |
| SNPDIR = "/project/yangili1/zpmu/covid19/data/hornet_snp" | |
| chrm = sorted([str(x) for x in range(1, 23)]) |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ggQQplot <- function(pList, colVec = c("black", "orange", "red", "purple"), | |
| legendLabel = NULL, title = "", openRange = F, sampling = 1) { | |
| if (is.null(legendLabel)) { | |
| legendLabel = colVec | |
| } | |
| if (length(pList) > length(colVec)) { | |
| stop("pList needs to be shorter than colVec!!!") | |
| } |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| getFDR <- function(Stat, Stat0) { | |
| m <- length(Stat) | |
| n <- length(Stat0) | |
| v <- c(rep(T, m), rep(F, n)) | |
| v <- v[order(c(Stat, Stat0), decreasing = T)] | |
| vSumT <- (m - cumsum(v == T)[v == T] + 1) / m | |
| vSumF <- (n - cumsum(v == F)[v == T]) / n | |
| fdr <- cummin(pmin(1, vSumF / vSumT)) | |
| fdr <- fdr[rank(-Stat)] | |
| return(fdr) |
Zepeng-Mu
/ find_loci.R
Created
April 21, 2022 20:22
Getting non-overlapping loci from GWAS for colocalization analysis
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| disjoinGr <- function(df, chr = "CHR", bp = "BP", pval = "Pval", snp = "SNP", size = 5e5) { | |
| inGr <- GRanges(df[[chr]], IRanges(df[[bp]] - size, df[[bp]] + size - 1), | |
| SNPID = df[[snp]], BP = df[[bp]], Pval = df[[pval]]) | |
| disjointGr <- disjoin(inGr) | |
| ov <- findOverlaps(resize(inGr, 1, "center"), disjointGr) | |
| hitGr <- disjointGr[subjectHits(ov)] | |
| ovGr <- setdiff(disjointGr, hitGr) | |
| firstHalf <- resize(ovGr, width(ovGr) / 2 - 1, "start") | |
| secondHalf <- resize(ovGr, width(ovGr) / 2, "end") |