Load user-supplied count matrices as metaXpressStudy objects

Constructs metaXpressStudy objects from local count matrix files and matching metadata files. Supports CSV, TSV, and RDS formats.

Usage

mx_load_local(
  count_paths,
  metadata_paths,
  accessions = NULL,
  organism = "Homo sapiens"
)

Arguments

count_paths

Character vector of file paths to count matrices. Each file must have genes as rows (with rownames) and samples as columns.

metadata_paths

Character vector of file paths to sample metadata tables. Each must contain at minimum condition and sample_id columns. Length must match count_paths.

accessions

Character vector of accession IDs (labels), one per study. Defaults to the basename of count_paths without extension.

organism

Character scalar. Species for all studies. Default: "Homo sapiens".

Value

A named list of metaXpressStudy objects.

See also

mx_fetch_geo, mx_qc_study

Examples

if (FALSE) { # \dontrun{
  studies <- mx_load_local(
    count_paths    = c("study1_counts.csv", "study2_counts.csv"),
    metadata_paths = c("study1_meta.csv",   "study2_meta.csv")
  )
} # }