filter_markers: Filter a dataframe with cluster markers.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Filter a dataframe with cluster markers.

Description

Filter a dataframe with cluster markers.

Usage

filter_markers(
  markers,
  top_n,
  top_n_wt = c("top", "fdr", "lfc", "auc"),
  distinct_by = NULL
)

Arguments

markers	A dataframe-like object.
top_n	A numeric scalar: number of top markers to keep.
top_n_wt	A character scalar: name of column in markers by which top markers will be determined: "top": the minimum rank across all pairwise comparisons. Only possible if markers were computed with pval.type="any". "fdr": False Discovery Rate "lfc": log2 fold change "auc": Area Under Curve. Only possible if marker test was "wilcox".
distinct_by	A character scalar: name of column in markers by which unique rows will be kept.

Value

A filtered markers object.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.