Load Track File to Dataframe.

LoadTrackFile(
  track.file,
  track.folder = NULL,
  format = c("bam", "wig", "bw", "bedgraph", "txt"),
  region = "chr14:21,677,306-21,737,601",
  extend = 2000,
  gtf.gr = NULL,
  gene.name = "HNRNPC",
  gene.name.type = c("gene_name", "gene_id"),
  meta.info = NULL,
  meta.file = "",
  bamcoverage.path = NULL,
  norm.method = c("RPKM", "CPM", "BPM", "RPGC", "None"),
  single.nuc = FALSE,
  single.nuc.region = NULL,
  bin.size = 10,
  bc.extra.para = NULL,
  n.cores = 1
)

Arguments

track.file	Track file, when `track.folder` is not NULL, determined by `track.folder`.
track.folder	Track file folder. Default: NULL.
format	Track file format, chosen from bam, wig, bw(bigwig), bedgraph(bedGraph) and txt.
region	Region used to create coverage plot, eg: chr14:21,677,306-21,737,601 or chr14:21,677,306. Default: "chr14:21,677,306-21,737,601"
extend	Extend length of `region`. Default: 2000.
gtf.gr	Granges object of GTF, created with `import.gff`. Default: NULL.
gene.name	The name of gene. Default: HNRNPC.
gene.name.type	Gene name type (filed of `gtf.gr`), chosen from gene_name and gene_id. Default: gene_name.
meta.info	Track file metadata. The columns should be: SampleName (`track.file` without suffix), Type (sample with replicates information), Group (sample group). when `meta.file` is not NULL, determined by `meta.file`.Default: NULL.
meta.file	File contains track file metadata. Default: "".
bamcoverage.path	The path to `bamCoverage`, used when `format` is bam. Default: NULL (auto-detect).
norm.method	Methods to normalize the number of reads per bin, chosen from "RPKM", "CPM", "BPM", "RPGC", "None". Default: RPKM.
single.nuc	Logical value, whether to visualize at single nucleotide level. Default: FALSE.
single.nuc.region	Region for `single.nuc`. Default: NULL
bin.size	Size of the bins, in bases. Default: 50.
bc.extra.para	Extra parameters for `bamCoverage`, eg: "--effectiveGenomeSize 2700000000 --ignoreForNormalization chrX"
n.cores	The number of cores to be used for this job. Default:1.

Value

A dataframe.

Examples

library(ggcoverage)
library(utils)
meta.file <- system.file("extdata", "RNA-seq", "meta_info.csv", package = "ggcoverage")
sample.meta <- utils::read.csv(meta.file)
# track folder
track.folder <- system.file("extdata", "RNA-seq", package = "ggcoverage")
# load bigwig file
track.df <- LoadTrackFile(
  track.folder = track.folder, format = "bw", region = "chr14:21,677,306-21,737,601",
  extend = 2000, meta.info = sample.meta
)