Retrieve Sequences — retrieve_seqs • TSRexploreR

Retrieve Sequences

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.