make_rnk: Make rank lists

Description Usage Arguments Value Examples

View source: R/make_rnk.R

Description

make_rnk() makes rank lists for pre-ranked geneset enrichment analysis.

Usage

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make_rnk(celltype, rank_df, gene_name, rank_stat, decreasing = T,
  write_rnk = F, output_dir = NULL, output_name = NULL)

Arguments

celltype

CellType to create rank lists for.

rank_df

a dataframe with the pre-requisite rank statistics

gene_name

column in rank_df containing gene names.

rank_stat

column in rank_df containing statistic to rank genes by.

decreasing

logical; whether to rank genes by decreasing value of rank_stat.

write_rnk

logical; whether to write .rnk files for GSEA

output_dir

name of directory to write .rnk files to; if directory does not exist, it will be created

output_name

prefix for .rnk file names; .rnk files will be named "output_name_celltype.rnk"

group_column

column name of column in annotation object with values corresponding to those in group_vector to use for computing logical columns. Defaults to NULL

Value

a list

Examples

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make_rnk(Rods, rank_df, "Gene_symbol", "Rank stat", decreasing =T, write_rnk=F)

jacobheng/cellwrangler documentation built on Aug. 12, 2019, 6:49 a.m.