searchSrrID: Search SRR accession IDs using projectID

In paodan/SRRDownloader: Download Raw Fastq Files from SRA Database.

Search SRR accession IDs using projectID

Description

Search SRR accession IDs using projectID

Usage

searchSrrID(projectID = "PRJNA540657", timeout = 60)

Arguments

projectID	character, the project accession ID to search in sra database (https://www.ncbi.nlm.nih.gov/sra). This ID can be searched by searchProjectID function.
timeout	numeric, the number of seconds to wait before killing the searching process.

Value

a SRR documents "runinfo" data frame containing 47 columns, which are Run, ReleaseDate, LoadDate, spots, bases, spots_with_mates, avgLength, size_MB, AssemblyName, download_path, Experiment, LibraryName, LibraryStrategy, LibrarySelection, LibrarySource, LibraryLayout, InsertSize, InsertDev, Platform, Model, SRAStudy, BioProject, Study_Pubmed_id, ProjectID, Sample, BioSample, SampleType, TaxID, ScientificName, SampleName, g1k_pop_code, source, g1k_analysis_group, Subject_ID, Sex, Disease, Tumor, Affection_Status, Analyte_Type, Histological_Type, Body_Site, CenterName, Submission, dbgap_study_accession, Consent, RunHash, and ReadHash.
Please note RunHash and ReadHash are not MD5SUM of each file.

Examples

{
## Not run: 
searchSrrID()
searchSrrID("PRJNA543132")

## End(Not run)
}

paodan/SRRDownloader documentation built on Aug. 25, 2023, 3:23 a.m.