RangerDE: RangerDE

In jspaezp/sctree: Tree based analysis of single rna-seq clusters

Description

A Helper function that interfaces with Seurat::FindMarkers

Usage

RangerDE(data.use, cells.1, cells.2, verbose, ...)

Arguments

data.use	sparse matrix passed by seurat
cells.1	barcode names of the cells asigned as cluster 1
cells.2	barcode names of the cells asigned as cluster 2
verbose	logical indicating wether the run should be verbose
...	additional arguments passed to sctree::ranger_importances.df

Examples

library(Seurat)
    library(sctree)
    head(FindMarkers(object = Seurat::pbmc_small,
    ident.1 = 0, test.use = 'RangerDE', warn.imp.method = FALSE))
#        importance p_val   gene  avg_logFC pct.1 pct.2 p_val_adj
# GNLY    0.4337917     0   GNLY  4.7841852 0.444 0.068         0
# CD7     0.3529089     0    CD7  2.5559735 0.528 0.091         0
# IL7R    0.1816056     0   IL7R  2.0708996 0.389 0.295         0
# NOSIP   0.2407237     0  NOSIP  2.0604084 0.444 0.250         0
# CCL5    0.5225574     0   CCL5  1.4914821 0.667 0.273         0
# LGALS1  0.3361842     0 LGALS1 -0.9457555 0.500 0.727         0

jspaezp/sctree documentation built on April 30, 2020, 10:36 p.m.