get_raw_metadata: Get all raw metadata from SRA

In SiruoWang/srametadata: Getting and cleaning metadata from Sequence Read Archive (SRA)

Description

Get all raw metadata from SRA associated with SRA accessions numbers

Usage

get_raw_metadata(run_accession = NULL, sample_accession = NULL,
  experiment_accession = NULL, study_accession = NULL,
  submission_accession = NULL, platform = NULL, db_conn)

Arguments

run_accession	A vector with run accessions
sample_accession	A vector with sample accessions
experiment_accession	A vector with experiment accessions
study_accession	A vector with study accessions
submission_accession	A vector with submission accessions
platform	Sequencing platform, e.g "ILLUMINA"
db_connn	Connection to the sqlite database

Value

A dataframe with all metadata associated with the filters provided to the function.

Examples

library('srametadata')

sqlfile <- file.path('.', 'SRAmetadb.sqlite')

# Create connection
conn <- dbConnect(SQLite(),sqlfile)

get_raw_metadata(run_accession = c("DRR023427", "SRR946066", "ERR204978"), 
                 experiment_accession = "SRX329581", 
                 sample_accession = c("SRS465599","DRS014276"),
                 study_accession = "SRP028344",
                 submission_accession = "SRA096347", 
                 platform = "ILLUMINA",
                 db_conn = conn)

get_raw_metadata(experiment_accession = "SRX329581", 
                 db_conn = conn)

get_raw_metadata(
    run_accession = c("DRR023427", "SRR946066", "ERR204978"), 
    db_conn = conn)

get_raw_metadata(
    sample_accession = c("SRS465599","DRS014276"),
    db_conn = conn)

all_illumina_sra <- get_raw_metadata(platform = "ILLUMINA", db_conn = conn)

SiruoWang/srametadata documentation built on May 9, 2019, 1:47 p.m.