rank_gse: This function will perform fast preranked gene set...

Description Usage Arguments Value

View source: R/rank_gse.R

Description

This function will perform fast preranked gene set encrichment analysis

Usage

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rank_gse(
  directory,
  rank_data,
  out_dir = "3_gse",
  from_gene,
  to_gene,
  cluster_name,
  rank_by = "logFC"
)

Arguments

directory

Directory to get gmt file

rank_data

This can be a Directory to get RDS file or directly passing in dataframe

out_dir

Output directory

from_gene

"ENSG" or "ENSMUSG" or "HGNC" or "MGI"

to_gene

"MGI" or HGNC

cluster_name

Cluster name that user want to do the geneset analysis on

rank_by

User defined data ranking by logFC, Pvalue, or sign_Pvalue (Default setting at logFC)

Value

Outputs dataframe from fgsea function


Chris-Cherry/sctools documentation built on Jan. 25, 2022, 2:19 p.m.