View source: R/from_crossmeta.R
from_crossmeta | R Documentation |
Convert a microarray ExpressionSet saved with 'crossmeta' into a format for direct usage in 'dseqr'.
from_crossmeta(gse_name, data_dir)
gse_name |
Name of GSE accession dataset, must be folder in data_dir |
data_dir |
directory that contains |
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)
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