Skip to contents

Resolve SRA inputs to a canonical run table

Source: R/sra_import.R
BascetResolveSra.Rd

Accepts direct SRR accessions, an .sralist, an existing RunInfo CSV/data frame, or an NCBI SRA query. The returned table always contains Run and cell, with cell defaulting to Run to avoid collisions. Other RunInfo columns are retained as a mapping table for later renaming.

Usage

BascetResolveSra(
  runs = NULL,
  sralist = NULL,
  runinfo = NULL,
  query = NULL,
  bioproject = NULL,
  terms = NULL,
  pageSize = 500,
  sleep = 1.2
)

Arguments

runs

Character vector of SRA run accessions.

sralist

Path to a file with one SRA run accession per line.

runinfo

SRA RunInfo data frame, or path to a RunInfo CSV file.

query

NCBI SRA query passed to rentrez.

bioproject

BioProject accession. Used to build a query when query is not provided.

terms

Additional NCBI SRA query terms joined with AND.

pageSize

Number of records fetched per E-utilities page.

sleep

Seconds to sleep between paged E-utilities fetches.

Value

A canonical SRA run table.