inst/script/ex_datasets.md

In steveped/extraChIPs: Additional functions for working with ChIP-Seq data

Creation of data objects

HiC Data

This was artificially generated using:

library(GenomicInteractions)
ex_hic <- GInteractions(
  GRanges("chr10:103880000-103882500"), 
  GRanges("chr10:103892500-103895000")
)
ex_hic$distance <- calculateDistances(ex_hic)

GRanges Objects

library(rtracklayer)
library(plyranges)
library(extraChIPs)
gr <- GRanges("chr10:103860000-103920000")
gtf <- import.gff("path/to/file", type = "gene")
ids <- subsetByOverlaps(gtf, gr)$gene_id
ex_genes <- subset(gtf, gene_id %in% ids) %>% 
  select(gene = gene_id, symbol = gene_name) %>% 
  reduceMC()

gtf <- import.gff("path/to/file", type = "exon")
ex_trans <- gtf %>%
  subset(gene_id %in% ids) %>% 
  as_tibble(rangeAsChar = FALSE) %>%
  group_by(transcript_id) %>%
  mutate(exon = paste0(transcript_id, "_", seq_along(transcript_id))) %>%
  makeGRangesFromDataFrame(keep.extra.columns = TRUE, seqinfo = sq) %>%
  mutate(feature = as.character(type)) %>%
  select(type, gene = gene_id, exon, transcript = transcript_id, symbol = gene_name) %>%
  sort() %>%
  setNames(.$transcript)

gtf <- import.gff("path/to/file", type = "transcript")
ex_prom <- gtf %>% 
  promoters(upstream = 1500, downstream = 500) %>% 
  reduce()

Bam Files

These represent ER binding data from the HCI-005 PDX taken from Hickey et al (2015) The androgen receptor is a tumor suppressor in estrogen receptor-positive breast cancer Nat Med, along with the Input sample. Regions were extracted using

samtools view -h filename.bam "chr10:103860000-103920000" > fileout.bam
samtools index fileout.bam

BigWig Files

BigWig files were created by taking bedGraph files as output by macs2 callpeak, converting to BigWig using the GRAVI workflow, loading into R then exporting using

fl <- BigWigFile(file.path("path_to_complete_bigwig"))
bw <- import.bw(fl, which = gr)
export.bw(bw, "path/to/output.bw")

Bed Files

This was taken as the merged sample macs2 callpeak output in narrowPeak format and restricted to the above range

peaks <- importPeaks("path/to/source.bed")
export.bed(subsetByOverlaps(peaks[[1]], gr), "path/to/output.bed.gz")

steveped/extraChIPs documentation built on Aug. 1, 2024, 12:36 a.m.