Download¶

Metadata¶

library(curatedMetagenomicData)
rowdata <- curatedMetagenomicData(
    "MetaCardis_2020_a.relative_abundance",
    dryrun = FALSE,
    rownames = "short"
)
data <- colData(rowdata[1](<../../../../blog/posts/1.md>))
dim(data)
write.csv(data, "metadata.csv", row.names = TRUE)

Feature Metadata¶

rowdata <- rowData(data_gene[1](<../../../../blog/posts/1.md>))
data <- as.data.frame(feature_info)
write.csv(data, "feature_metadata.csv", row.names = TRUE)

Feature-Sample Matrix¶

assayNames(se_object)

data <- assays(se_object)[["relative_abundance"]]
write.csv(data, "gene_families.csv", row.names=TRUE)