Workflow Steps and Code Snippets

2 tagged steps and code snippets that match keyword Homo.sapiens

Code used for the manuscript 'Network reconstruction for trans acting genetic loci using multi-omics data and prior information' by Hawe et al., 2022 in Genome Medicine 

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log <- file(snakemake@log[[1]], open="wt")
sink(log)
sink(log, type="message")

# ------------------------------------------------------------------------------
print("Load libraries and source scripts.")
# ------------------------------------------------------------------------------
library(qvalue)
library(data.table)
library(graph)
library(fdrtool)
library(Homo.sapiens)
library(pheatmap)

source("scripts/lib.R")
source("scripts/priors.R")

# ------------------------------------------------------------------------------
print("Get snakemake params.")
# ------------------------------------------------------------------------------
# input
fgene_priors <- snakemake@input[["gg_priors"]]
feqtlgen_eqtl_priors <- snakemake@input[["eqtlgen_eqtl_priors"]]
fgtex_eqtl_priors <- snakemake@input[["gtex_eqtl_priors"]]
fcpgcontext <- snakemake@input[["cpg_context"]]
ftsscontext <- snakemake@input[["tss_context"]]
fppi <- snakemake@input[["ppi"]]
franges <- snakemake@input[["ranges"]]
fcpg_annot <- snakemake@input[["cpg_annot"]]

# params
sentinel <- snakemake@wildcards$sentinel
eqtl_prior_type <- snakemake@params$eqtl_prior_type

# output
fout <- snakemake@output[[1]]
fplot <- snakemake@output[[2]]

# ------------------------------------------------------------------------------
print("Loading data.")
# ------------------------------------------------------------------------------

print("Loading PPI db.")
ppi_db <- readRDS(fppi)

# load ranges object
ranges <- readRDS(franges)

# get all entities as single vector
nodes <- c(sentinel, ranges$snp_genes$SYMBOL,
           ranges$tfs$SYMBOL, ranges$spath$SYMBOL)

if(ranges$seed == "meqtl") {
  nodes <- c(nodes, with(ranges,
                         c(cpg_genes$SYMBOL, names(cpgs))))
} else {
  nodes <- c(nodes, ranges$trans_genes$SYMBOL)
}
nodes <- unique(nodes)

# ------------------------------------------------------------------------------
print("Load gtex priors, extract link priors.")
# ------------------------------------------------------------------------------
feqtl <- ifelse("eqtlgen" %in% eqtl_prior_type, 
                feqtlgen_eqtl_priors, 
                fgtex_eqtl_priors)
load_eqtl_priors(sentinel, feqtl, eqtl_prior_type)
load_genegene_priors(fgene_priors)

# set appropriate context
if(ranges$seed == "meqtl") {
  fcontext <- fcpgcontext
} else {
  fcontext <- ftsscontext
}

print("Annotation context is:")
print(fcontext)

print("Retrieving link priors.")
pr <- get_link_priors(ranges, nodes, ppi_db, fcontext, 
                      fcpg_annot)

# create a heatmap to be able to look at the priors
pheatmap(filename = fplot, pr, cex=0.7)

# ------------------------------------------------------------------------------
print("Saving data.")
# ------------------------------------------------------------------------------
saveRDS(pr, file=fout)
R Snakemake data.table Homo.sapiens pheatmap graph qvalue fdrtool From line 6 of scripts/collect_priors.R 
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log <- file(snakemake@log[[1]], open = "wt")
sink(log)
sink(log, type = "message")

# ------------------------------------------------------------------------------
# Load libraries and source scripts
# ------------------------------------------------------------------------------
suppressPackageStartupMessages(library(qvalue))
suppressPackageStartupMessages(library(data.table))
suppressPackageStartupMessages(library(graph))
suppressPackageStartupMessages(library(parallel))
suppressPackageStartupMessages(library(fdrtool))
suppressPackageStartupMessages(library(Homo.sapiens))
suppressPackageStartupMessages(library(rtracklayer))
suppressPackageStartupMessages(library(FDb.InfiniumMethylation.hg19))
source("scripts/lib.R")
source("scripts/priors.R")

# ------------------------------------------------------------------------------
# Get snakemake params
# ------------------------------------------------------------------------------

# inputs
feqtl <- snakemake@input[["eqtl"]]
fsnpinfo <- snakemake@input[["snpinfo"]]
fexpr <- snakemake@input[["expr"]]
fsampleinfo <- snakemake@input[["sampleinfo"]]
fpheno <- snakemake@input[["pheno"]]
fppi <- snakemake@input[["ppi"]]
dplots <- snakemake@params$plot_dir

# outputs
fout_gene_priors <- snakemake@output$gene_priors
fout_eqtl_priors <- snakemake@output$eqtl_priors

# ------------------------------------------------------------------------------
# Start processing
# ------------------------------------------------------------------------------

print("Loading PPI db.")
ppi_db <- readRDS(fppi)

# simply delegate
create_priors(
  feqtl,
  fsnpinfo,
  fexpr,
  fsampleinfo,
  fpheno,
  dplots,
  ppi_db,
  fout_gene_priors,
  fout_eqtl_priors
)

if (FALSE) {
  # ------------------------------------------------------------------------------
  print("Prepare the Banovich based priors, i.e. TF-CpG priors.")
  # ------------------------------------------------------------------------------
  # methylation data
  meth <-
    fread("data/current/banovich-2017/methylation/full_matrix.txt",
          data.table = F)
  rownames(meth) <- meth$V1
  meth$V1 <- NULL
  cpgs <- features(FDb.InfiniumMethylation.hg19)
  cpgs <- cpgs[rownames(meth)]

  # expression data
  expr <-
    read.table(
      "data/current/banovich-2017/xun_lan/allTFexp.withHeader",
      header = T,
      sep = "\t",
      stringsAsFactors = F
    )

  # apparently the table contains duplicated entries, remove them
  expr <- expr[!duplicated(expr), ]
  rownames(expr) <- unique(expr[, 1])

  samples <- intersect(colnames(expr), colnames(meth))

  expr <- t(expr[, samples])
  meth <- t(meth[, samples])

  # ------------------------------------------------------------------------------
  print("Get (our) chip-seq context for the cpgs.")
  # ------------------------------------------------------------------------------
  tfbs_ann <- get_tfbs_context(names(cpgs), fcpgcontext)

  # ------------------------------------------------------------------------------
  print("For each TF, get the correlation to each of the CpGs it is bound nearby")
  # ------------------------------------------------------------------------------
  pairs <- lapply(colnames(expr), function(tf) {
    # get columns for tf
    sub <-
      tfbs_ann[, grepl(tf, colnames(tfbs_ann), ignore.case = T), drop = F]
    rs <- rowSums(sub)
    bound_cpgs <- names(rs[rs > 0])

    assoc <- unlist(mclapply(bound_cpgs, function(c) {
      cor.test(expr[, tf],
               meth[, c],
               method = "pearson")$p.value
    }, mc.cores = threads))

    cbind.data.frame(
      TF = rep(tf, length(assoc)),
      CpG = bound_cpgs,
      rho = assoc,
      stringsAsFactors = F
    )
  })

  # ------------------------------------------------------------------------------
  print("Collect and finalize results.")
  # ------------------------------------------------------------------------------
  tab <- do.call(rbind, pairs)
  colnames(tab) <- c("TF", "CpG", "pval")
  tab$qval <- qvalue(tab$pval)$lfdr
  tab$prior <- 1 - tab$qval
  head(tab)
  write.table(
    file = "results/current/tf-cpg-prior.txt",
    sep = "\t",
    col.names = NA,
    row.names = T,
    quote = F,
    tab
  )
}
# ------------------------------------------------------------------------------
print("Session info:")
# ------------------------------------------------------------------------------
sessionInfo()
R Snakemake data.table FDb.InfiniumMethylation.hg19 Homo.sapiens graph qvalue fdrtool From line 7 of scripts/create_priors.R
data / bioconductor

Homo.sapiens

Annotation package for the Homo.sapiens object: Contains the Homo.sapiens object to access data from several related annotation packages.

author: Bioconductor Core Team
library: r:Homo.sapiens
license: Artistic-2.0
version: 1.3.1
biocViews: ['AnnotationData', 'Genetics', 'Homo_sapiens', 'OrganismDb']
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