retrieve_seqs: Retrieve Sequences
In zentnerlab/TSRexploreR: TSS and TSR Analysis

retrieve_seqs

R 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.