create_sample_info: Search the SRA database and create a data frame of sample...

In almeidasilvaf/GEAtlas: Building Expression Atlas from RNA-Seq data

Search the SRA database and create a data frame of sample metadata

Description

Search the SRA database and create a data frame of sample metadata

Usage

create_sample_info(term, retmax = 5000)

Arguments

term	Character with the search term, e.g. "Glycine max[ORGN] AND RNA-seq[STRA]".
retmax	Numeric with the maximum number of hits returned by the search.

Value

A data frame with the following columns:

BioSample

BioSample accession.

Experiment

Experiment accession (SRX*).

Run

Run accession (SRR*).

Tissue

Tissue from which RNA was extracted.

Pubmed

Pubmed ID of articles associated with the project, if any.

BioProject

Bioproject accession.

Instrument

Sequencing instrument

Layout

Library layout (single- or paired-end sequencing).

Selection_method

Library selection method.

SRA_sample

SRA sample accession (SRS*).

SRA_study

SRA study accession (SRP*).

Treatment

Treatment for the biosample.

Cultivar

Plant cultivar.

Study_title

Study title, if any.

Study_abstract

Study abstract, if any.

Date

Date of release.

Origin

Country of origin.

Examples

term <- "SAMN02422669[BSPL]"
df <- create_sample_info(term)

almeidasilvaf/GEAtlas documentation built on April 14, 2023, 6:58 p.m.