In CharlesJB/metageneInputs: Create input files for metagene article

library(metageneInputs)
library(ENCODExplorer)

Introduction

The goal of this vignette is to produce the groups of regions that will be used for the metagene paper.

All the files produced will be save inside a temporary directory and will need to be moved manually:

outdir <- paste0("/tmp/", basename(tempfile("")))
dir.create(outdir)
outdir

Regions

To obtain the robust regoins, we need to keep only the regions that overlap with the TSS from the FantomTSS.hg19 package and then extract the mean TPM value for each regions.

Robust enhancer regions

cell_line <- "GM12878"
robust_enhancer_regions <- get_robust_enhancer_regions(cell_line,
                                                        keep_y = FALSE)
robust_enhancer_regions

Robust promoter regions

robust_promoter_regions <- get_robust_promoter_regions(cell_line,
                                                        keep_y = FALSE)
robust_promoter_regions

Tresholds

In order to split promoters and enhancers into 5 different groups based on their expression level in TPM, we will first calculate tresholds for each groups using every TPM values from every non-zero robust TSS TPM of Fantom5 except those from the r cell_line.

fantom_tpm <- get_all_tss_tpm(exclude = cell_line)
probs <- seq(1.0, 0, -0.25)
quantiles <- quantile(fantom_tpm[fantom_tpm != 0], probs = probs)
quantiles

Split the regions

The enhancers:

enhancers <- split_by_quantiles(robust_enhancer_regions, quantile, cell_line)
enhancers

The promoters:

promoters <- split_by_quantiles(robust_promoter_regions, quantile, cell_line)
promoters

Save results:

outfile <- paste0(outdir, "/splitted_regions.RData")
save(enhancers, promoters, file = outfile)

TPM GRangesList

GenomicRanges::mcols(robust_promoter_regions)[["gene_id"]] <- NULL
TPM <- GenomicRanges::GRangesList(enhancers = robust_enhancer_regions,
                                  promoters = robust_promoter_regions)
outfile <- paste0(outdir, "/tpm_grangeslist.RData")
save(TPM, file = outfile)

CharlesJB/metageneInputs documentation built on May 6, 2019, 9:58 a.m.