Remove studies that fail quality control

Keeps studies according to the per-criterion QC results from mx_qc_study. Failures, not the summed score, drive the decision, because criteria that cannot be evaluated (common for GEO data) should not count against a study.

Usage

mx_filter_studies(
  studies,
  required = c(1, 7, 10),
  max_failed = Inf,
  qc_threshold = NULL
)

Arguments

studies

A named list of metaXpressStudy objects after mx_qc_study.

required

Integer vector of criteria that must not fail. Default: c(1, 7, 10) (>= 3 samples per group, complete condition labels, raw counts) – the minimum for valid count-based DE.

max_failed

Integer. Maximum number of other failed criteria allowed. Default: Inf (only required criteria exclude).

qc_threshold

Optional minimum qc_score (criteria passed). Default NULL: not used.

Value

The filtered list. A message lists removed studies and reasons.

Examples

if (requireNamespace("airway", quietly = TRUE)) {
  data("airway", package = "airway")
  s <- mx_qc_study(mx_from_se(airway, condition_col = "dex",
                              accession = "GSE52778"))
  length(mx_filter_studies(list(airway = s)))
}
#> [1] 1