findDynGenes: find genes expressed dynamically

Description Usage Arguments Value

View source: R/1_GRN.R

Description

uses slingshot approach

Usage

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findDynGenes(
  expDat,
  sampTab,
  path = NULL,
  group_column = "dpt_groups",
  pseudotime_column = "pseudotime",
  method = "gam",
  expRaw = NULL
)

Arguments

expDat

properly normalized expression matrix

sampTab

sample table that includes pseudotime, rownames = cell_name, and a group column

path

vector of group names to include

group_column

column name in sampTab annotating groups in the path

pseudotime_column

column name in sampTab annotating pseudotime or latent time

method

method to find dynamic genes. Defaults to "gam", if "tradeseq", must provide expRaw

expRaw

raw expression matrix, required if method="tradeseq"

Value

pvals and cell info


pcahan1/epoch documentation built on Feb. 14, 2022, 1:57 a.m.