mcell_mat_rpt_cor_anchors: Find and report naive gene gene correlation over umi matrix

In tanaylab/metacell: Meta cell analysis for single cell RNA-seq data

Find and report naive gene gene correlation over umi matrix

Description

The generated table should be the basis for manual curation usually, and can be used to generate supervised gene sets, or a basis for them

Usage

mcell_mat_rpt_cor_anchors(
  mat_id,
  gene_anchors,
  gene_anti = c(),
  cor_thresh,
  tab_fn,
  sz_cor_thresh = NA,
  downsample_n = NA,
  cells = NULL
)

Arguments

mat_id	matrix to use
gene_anchors	genes that will be used as anchors for computing correlation against all other genes
gene_anti	genes that will be used as negative anchors - high correlation to these will be considered negatively
cor_thresh	correlation threshold (on downsampled data) - the table will include genes with maximal correlation higher than the threshold, AND, maximal correlation for negative anchor lower than for positive nachors
tab_fn	file name of tabular report

tanaylab/metacell documentation built on Jan. 29, 2025, 1:34 a.m.