from_crossmeta: Covert from crossmeta to dseqr formats

In hms-dbmi/drugseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

Covert from crossmeta to dseqr formats

Description

Convert a microarray ExpressionSet saved with 'crossmeta' into a format for direct usage in 'dseqr'.

Usage

from_crossmeta(gse_name, data_dir)

Arguments

gse_name	Name of GSE accession dataset, must be folder in data_dir
data_dir	directory that contains gse_name folder

Examples

library(Biobase)

# generate example eset
sd <- 0.3*sqrt(4/rchisq(1000,df=4))
y <- matrix(rnorm(1000*6,sd=sd),1000,6)
rownames(y) <- paste("Gene",1:1000)
y[1:2,4:6] <- y[1:2,4:6] + 2

y[100:200, c(1,2,6)] <- y[100:200, c(1,2,6)] + 0.5

pdata <- data.frame(group = c(rep('healthy', 3), rep('disease', 3)))
fdata <- data.frame(SYMBOL = row.names(y),
                   PROBE = row.names(y),
                   row.names = row.names(y))

eset <- ExpressionSet(y,
                     phenoData = as(pdata, 'AnnotatedDataFrame'),
                     featureData = as(fdata, 'AnnotatedDataFrame'))


# save
eset <- list(GSE1=eset)
data_dir <- tempdir()
gse_dir <- file.path(data_dir, 'GSE1')
dir.create(gse_dir)
saveRDS(eset, file.path(gse_dir, 'GSE1_eset.rds'))

from_crossmeta('GSE1', data_dir)

hms-dbmi/drugseqr documentation built on Feb. 15, 2024, 10:38 p.m.