search_field: Get metadata from SRA

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

Description

This function grabs metadata from the sample, experiment, study and experiment attribute in the SRA metadata database.

Usage

search_field(runacc, field, type, db_conn)

Arguments

runacc	A vector with run accessions
field	A string specifying the field of interest (e.g. "sex", "cell_line", "tissue")
type	Type of metadata which is associated with runs: 'sample', 'experiment', 'study' or 'run'
db_conn	Connection to the sqlite database

Value

resfield A dataframe with run_accessions and values associated with the field of interest. If field does not exist, NAs are returned

Examples

search_field(runacc = c("DRR023427", "SRR946066", "ERR204978"),  
           field = "disease", 
           type = "sample",
           db_con = conn)

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