Filter lowly expressed genes — rs_filter_by

edgeR's filterByExpr, via the edge-rs crate.

Usage

rs_filter_by_expr(
  counts,
  group,
  lib_size,
  min_count,
  min_total_count,
  min_prop
)

counts: Integer or double matrix. Raw counts of genes x samples.
group: Integer vector or NULL. 1-based group code per sample (e.g. as.integer(factor(x))). If NULL, all samples form one group.
lib_size: Numeric vector or NULL. Library size per sample. NULL uses the column sums.
min_count: Numeric. Minimum count in the median-sized library.
min_total_count: Numeric. Minimum total count across all samples.
min_prop: Numeric. Fraction of the smallest group size beyond edgeR's large.n that still has to express the gene.

Boolean vector, one per gene. TRUE if the gene is kept.

Chen, Lun and Smyth, F1000Research, 2016