The metaXpressStudy class

Represents a single bulk RNA-seq study. metaXpressStudy extends SummarizedExperiment, so raw counts live in the "counts" assay, sample metadata in colData(), and optional gene annotation in rowData(). All standard SummarizedExperiment accessors and subsetting (study[genes, samples], study$condition) work directly. Populated by mx_fetch_geo, mx_fetch_sra, mx_load_local, or mx_from_se.

Details

The colData must contain a condition column (case/control labels) once an accession is set.

Slots

accession

A length-1 character giving the GEO/SRA accession ID (e.g., "GSE12345") or "local" for user-supplied data.

organism

A length-1 character giving the species (e.g., "Homo sapiens").

qc_score

A length-1 numeric in [0, 10]. Filled by mx_qc_study; NA until then.

de_result

A data.frame of per-study differential expression results. Empty until mx_de is called. Required columns when populated: gene_id, log2FC, pvalue, padj, baseMean.

See also

metaXpressStudy, mx_from_se, mx_fetch_geo, mx_qc_study, mx_de