Package 'GEOfastq'

Title: Downloads ENA Fastqs With GEO Accessions
Description: GEOfastq is used to download fastq files from the European Nucleotide Archive (ENA) starting with an accession from the Gene Expression Omnibus (GEO). To do this, sample metadata is retrieved from GEO and the Sequence Read Archive (SRA). SRA run accessions are then used to construct FTP and aspera download links for fastq files generated by the ENA.
Authors: Alex Pickering [cre, aut]
Maintainer: Alex Pickering <[email protected]>
License: MIT + file LICENSE
Version: 1.13.0
Built: 2024-06-30 03:42:07 UTC
Source: https://github.com/bioc/GEOfastq

Help Index

Get GSE text from GEO

Description

Get GSE text from GEO

Usage

crawl_gse(gse_name)

Arguments

gse_name

GEO study name to get metadata for

Value

Character vector of lines on GSE record.

Examples

gse_text <- crawl_gse('GSE111459')

Crawls SRX pages for each GSM to get metadata.

Description

Goes to each GSM page to get SRX then to each SRX page to get some more metadata.

Usage

crawl_gsms(gsm_names, max.workers = 50)

Arguments

gsm_names

Character vector of GSMs.
max.workers

Maximum number of parallel workers to split task betweem

Value

data.frame

Examples

srp_meta <- crawl_gsms("GSM3031462")

# returns NULL because records on dbGAP for privacy reasons
srp_meta <- crawl_gsms("GSM2439650")

# example with empty values
srp_meta <- crawl_gsms('GSM4043025')

Extract GSMs needed to download RNA-seq data for a series

Description

Extract GSMs needed to download RNA-seq data for a series

Usage

extract_gsms(gse_text)

Arguments

gse_text

GSE text returned from crawl_gse

Value

Character vector of sample GSMs for the series gse_name

Examples

gse_text <- crawl_gse('GSE111459')
gsm_names <- extract_gsms(gse_text)

Gets part of path to download bulk RNAseq sample from EBI or NCBI

Description

Gets part of path to download bulk RNAseq sample from EBI or NCBI

Usage

get_dldir(srr, type = c("ebi", "ncbi"))

Arguments

srr

SRR/ERR run name
type

Either 'ebi' or 'ncbi'

Value

String path used by get_fastqs.

Examples

get_dldir('SRR014242')

Download and RNA-seq fastq data from EBI

Description

First tries to get RNA-Seq fastq files from EBI.

Usage

get_fastqs(srp_meta, data_dir, method = c("ftp", "aspera"), max_rate = "1g")

Arguments

srp_meta

data.frame with SRP meta info. Returned from crawl_gsms.
data_dir

Path to folder that fastq files will be downloaded to. Will be created if doesn't exist.
method

One of 'aspera' or 'ftp'. 'aspera' is generally faster but requires the ascp command line utility to be on your path and in the authors experience frequently stalls.
max_rate

Used when method = 'aspera' only. Sets the target transfer rate. The default is '300m'.

Value

Named vector of integer return codes from ascp or download.file. Names are SRR runs.

Examples

gsm_name <- 'GSM3926903'
srp_meta <- crawl_gsms(gsm_name)
data_dir <- tempdir()
res <- get_fastqs(srp_meta, data_dir)