AnnotatePeaksFromGTF: Annotates a set of peak coordinates from a GTF

In VCCRI/Sierra: PolyA counting and differential transcript usage analysis for scRNA-seq data

Annotates a set of peak coordinates from a GTF

Description

Annotate a set of peak coordinates according to genomic features the coordinates fall on - 3'UTR, exon, intron and 5'UTR, and annotate proximity to motifs. Motifs include the canonical polyA motif, A-rich regions and T-rich regions.

Usage

AnnotatePeaksFromGTF(
  peak.sites.file,
  gtf.file,
  output.file,
  genome = NULL,
  invert_strand = FALSE,
  annotationType = "any",
  transcriptDetails = TRUE,
  annotation_correction = TRUE,
  pA_motif_max_position = 50,
  AAA_motif_min_position = 10,
  polystretch_length = 13,
  max_mismatch = 1,
  append.chr.peaks = TRUE,
  check.chr = TRUE
)

Arguments

peak.sites.file	a file of peak coordinates.
gtf.file	GTF reference file.
output.file	file to write the annotations to.
genome	genome object. If NOT NULL then will perform pA motif analysis.
invert_strand	Boolean to signifiy if strand of gr peaks should be inversed
annotationType	can be assigned "any" or "within". Default is "any" which states that the peak with gr must overlap annotation feature (eg exon)
transcriptDetails	Boolean. If false will only return gene name. If true will return internal transcript position feature (eg exon/intron)
annotation_correction	Boolean. When multiple overlapping genes are identified will prioritise gene based on annotation. 3'UTR annotation trumps all other annotation.
pA_motif_max_position	Any AAUAAA after this position are not considered (default 50nt)
AAA_motif_min_position	Any polyA/polyT stretches before this postion are not considered (default 10)
polystretch_length	: the length of A or T to search for (default 13)
max_mismatch	number of allowed mismatches for motif matching (default 1)
append.chr.peaks	: When TRUE (default) appends the character "chr" on chromosome entry in peaks file.
check.chr	if TRUE (default) and append.chr.peaks is also TRUE, check whether "chr" characters have already been added.

Value

NULL. writes output to file

Examples

extdata_path <- system.file("extdata",package = "Sierra")
peak.merge.output.file <- paste0(extdata_path, "/TIP_merged_peaks.txt")
reference.file <- paste0(extdata_path,"/Vignette_cellranger_genes_subset.gtf")


 genome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10


 AnnotatePeaksFromGTF(peak.sites.file = peak.merge.output.file, 
                    gtf.file = reference.file, 
                    output.file = "TIP_merged_peak_annotations.txt", 
                    genome = genome)

VCCRI/Sierra documentation built on July 3, 2023, 6:39 a.m.