geo_characteristics: Build a data.frame from GEO's charactersitics for a given...

In leekgroup/recount: Explore and download data from the recount project

Build a data.frame from GEO's charactersitics for a given sample

Description

This function builds a data.frame from the GEO characteristics extracted for a given sample. The names of the of columns correspond to the field names. For a given SRA project, this information can be combined for all samples as shown in the examples section.

Usage

geo_characteristics(pheno)

Arguments

pheno

A DataFrame-class as created by geo_info.

Value

A 1 row data.frame with the characteristic fields as column names and the values as the entries on the first row. If the authors of the study used the same names for all samples, you can then combine them using rbind.

Author(s)

Leonardo Collado-Torres

Examples

## Load required library
library("SummarizedExperiment")

## Get the GEO accession ids
# geoids <- sapply(colData(rse_gene_SRP009615)$run[1:2], find_geo)
## The previous example code works nearly all the time but it
## can occassionally fail depending on how rentrez is doing.
## This code makes sure that the example code runs.
geoids <- tryCatch(
    sapply(colData(rse_gene_SRP009615)$run[1:2], find_geo),
    error = function(e) {
        c(
            "SRR387777" = "GSM836270",
            "SRR387778" = "GSM836271"
        )
    }
)

## Get the data from GEO
geodata <- do.call(rbind, sapply(geoids, geo_info))

## Add characteristics in a way that we can access easily later on
geodata <- cbind(geodata, geo_characteristics(geodata))

## Explore the original characteristics and the result from
## geo_characteristics()
geodata[, c("characteristics", "cells", "shrna.expression", "treatment")]

leekgroup/recount documentation built on May 24, 2024, 11:19 a.m.