README.md

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

Example

srametadata R package

srametadata is an R package for getting metadata from Sequence Read Archive (SRA) and making traits prediction.

Installation

devtools::install_github("SiruoWang/srametadata")

Package can be loaded into R as follows:

library('srametadata')

Getting started

Example: Get fastq urls from SRA.

library('srametadata')

# Get sqlite database
download_sra_db()

# Get path to sqlite database
sqlfile <- file.path('.', 'SRAmetadb.sqlite')

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

# one file, two files and three files associated with corresponding run accessions
get_fastq_urls(runacc = c("DRR001482", "DRR001627", "ERR204978"), db_con = conn)

Example: predict sex from SRA using run accessions.

predictsex(run_accession = "SRR1296065")
predictsex(run_accession = c("SRR1296065","SRR1044429"))

Example: normalize gene expression from SRA.

normalized(file = scan("sra_samples.txt", what="", sep="\n"), path = path, chr = "chrY", start = 14813160, end = 14972768)

Bug reports

Report bugs and issues on this Repository

Contributors

• Siruo (Sara) Wang
• Jose Alquicira Hernandez

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