make_se_object: Make SummarizedExperiment object

In szymczak-lab/harmonizeGeneExprData: Harmonization of gene expression data from GEO and ArrayExpress

Make SummarizedExperiment object

Description

Combine expression data, phenotype data, gene annotation and meta data into SummarizedExperiment object including checks on samples and genes.

Usage

make_se_object(pheno, meta.data.l = NULL, assays, anno = NULL)

Arguments

pheno	[data.frame] phenotype data
meta.data.l	[list] meta data (as extracted by extract_meta_data)
assays	[list] matrices of gene expression data, e.g. raw and voom transformed counts for RNAseq (as prepared by prepare_count_data)) or raw and SCAN normalized expression values for array data (as prepared by prepare_array_data))
anno	[data.frame] gene annotation (e.g. gene identifier, chromosomal position, gene names) with genes in rows and information in columns

Value

[SummarizedExperiment object] as generated by SummarizedExperiment

szymczak-lab/harmonizeGeneExprData documentation built on Dec. 1, 2022, 9:07 p.m.