retrieve_seqs: Retrieve Sequences

View source: R/sequences.R

retrieve_seqsR Documentation

Retrieve Sequences

Description

Retrieve Sequences

Usage

retrieve_seqs(
  experiment,
  data_type = c("tss", "tsr", "shift"),
  samples = "all",
  genome_assembly = NULL,
  threshold = NULL,
  dominant = FALSE,
  fixed_size = FALSE,
  extend_upstream = NULL,
  extend_downstream = NULL,
  return_format = "biostrings",
  output_dir = NULL
)

Arguments

experiment

TSRexploreR object.

data_type

Get sequences around TSSs ('tss'), TSRs ('tsr'), or TSS shifting results ('shift').

samples

A vector of sample names to analyze.

genome_assembly

Genome assembly in FASTA or BSgenome format.

threshold

TSSs or TSRs with a score below this value will not be considered.

dominant

If TRUE, will only consider the highest-scoring TSS per gene, transcript, or TSR or highest-scoring TSR per gene or transcript.

fixed_size

Whether all returned sequences should have the same fixed size starting from the center of the ranges.

extend_upstream

Distance to extend ranges upstream.

extend_downstream

Distance to extend ranges downstream.

return_format

Either 'table' or 'biostrings'.

output_dir

If set, the results will be saved to this directory. If return format is set to 'biostrings' the sequences will be saved as FASTA files. If return format is a table, it will be saved as a tab delimited table.


zentnerlab/TSRexploreR documentation built on Dec. 30, 2022, 10:27 p.m.