Description Usage Arguments Value Examples
View source: R/get_raw_metadata.R
Get all raw metadata from SRA associated with SRA accessions numbers
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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 |
A dataframe with all metadata associated with the filters provided to the function.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | 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)
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