extractCoverageData: Extract read coverage data from the bigWig files

In kauralasoo/wiggleplotr: Make read coverage plots from BigWig files

Extract read coverage data from the bigWig files

Description

Does not work on Windows, because rtracklayer cannot read BigWig files on Windows.

Usage

extractCoverageData(
  exons,
  cdss = NULL,
  transcript_annotations = NULL,
  track_data,
  rescale_introns = TRUE,
  new_intron_length = 50,
  flanking_length = c(50, 50),
  plot_fraction = 0.1,
  mean_only = TRUE,
  region_coords = NULL
)

Arguments

exons	list of GRanges objects, each object containing exons for one transcript. The list must have names that correspond to transcript_id column in transcript_annotations data.frame.
cdss	list of GRanges objects, each object containing the coding regions (CDS) of a single transcript. The list must have names that correspond to transcript_id column in trancsript_annotations data.frame. If cdss is not specified then exons list will be used for both arguments. (default: NULL).
transcript_annotations	Data frame with at least three columns: transcript_id, gene_name, strand. Used to construct transcript labels. (default: NULL)
track_data	data.frame with the metadata for the bigWig read coverage files. Must contain the following columns: sample_id - unique id for each sample. track_id - if multiple samples (bigWig files) have the same track_id they will be overlayed on the same plot, track_id is also used as the facet label on the right. bigWig - path to the bigWig file. scaling_factor - normalisation factor for each sample, useful if different samples sequenced to different depth and bigWig files not normalised for that. colour_group - additional column to group samples into, is used as the colour of the coverage track.
rescale_introns	Specifies if the introns should be scaled to fixed length or not. (default: TRUE)
new_intron_length	length (bp) of introns after scaling. (default: 50)
flanking_length	Lengths of the flanking regions upstream and downstream of the gene. (default: c(50,50))
plot_fraction	Size of the random sub-sample of points used to plot coverage (between 0 and 1). Smaller values make plotting significantly faster. (default: 0.1)
mean_only	Plot only mean coverage within each combination of track_id and colour_group values. Useful for example for plotting mean coverage stratified by genotype (which is specified in the colour_group column) (default: TRUE).
region_coords	Start and end coordinates of the region to plot, overrides flanking_length parameter. The 'both' option tends to give better results for wide regions. (default: area).

Value

List containing all of the necessary data for the plotCoverageData function ()

Examples

require("dplyr")
require("GenomicRanges")
sample_data = dplyr::data_frame(sample_id = c("aipt_A", "aipt_C", "bima_A", "bima_C"), 
    condition = factor(c("Naive", "LPS", "Naive", "LPS"), levels = c("Naive", "LPS")), 
    scaling_factor = 1) %>%
    dplyr::mutate(bigWig = system.file("extdata",  paste0(sample_id, ".str2.bw"), package = "wiggleplotr"))

track_data = dplyr::mutate(sample_data, track_id = condition, colour_group = condition)

selected_transcripts = c("ENST00000438495", "ENST00000392477") #Plot only two transcripts of the gens
## Not run: 
extractCoverageData(ncoa7_exons[selected_transcripts], ncoa7_cdss[selected_transcripts], ncoa7_metadata, track_data)

## End(Not run)

kauralasoo/wiggleplotr documentation built on July 4, 2022, 11:43 a.m.