Zepeng (Phoenix) Mu Zepeng-Mu
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Zepeng-Mu
/ tpManhattanSingle.R
Created
June 1, 2025 18:22
Create a single Manhattan plot using the tidyplots package
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| tpManhattanSingle <- function( | |
| summ.1, chr = "CHR", bp = "BP", p = "P", snp = "SNP", | |
| summ.1.name = "$-log[10](P)$", plot.label = NULL, | |
| logp = TRUE, size = 2, lead.snp = NULL, r2 = NULL, | |
| plot.width = 100, plot.height = 50, ... | |
| ) { | |
| 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 { |
Zepeng-Mu
/ Rstudio snippets
Created
May 18, 2025 01:04
Attach this to the end of Snippets in RStudio -> Tools -> Global options -> Code -> Edit snippets.
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| snippet script_header | |
| ################################################################################ | |
| ## Script Purpose: ${0} | |
| ## Author:Zepeng Mu ([email protected]) | |
| ## Date: `r format(Sys.time(), "%a, %b %e %Y")` | |
| ################################################################################ | |
| snippet h1 | |
| # ${0:Header1} ---- | |
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| 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]]) |
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| ## 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)]) | |
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| 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!!!") | |
| } |
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| 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
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| 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") |