seekGSErl: creates a ranked list from diff.Expression data

In Solatar/seeqR:

Description

creates a ranked list from diff.Expression data

Usage

seekGSErl(
  DE,
  pFilter = NA,
  colentrez = "entrezid",
  colrank = "log2FC",
  colp = "padj"
)

Arguments

DE	a data.frame with a column "log2FC" and entrezids as rownames. Optionally a "padj" column if pFilter is to be used.
pFilter	float, cutoff below which genes are excluded from the list (takes colp to determine which column to filter)
colentrez	string, name of column containing entrezids
colrank	string, name of column values should be ranked after (high to low)
colp	string, name of column by which the pFilter operates

Value

A sorted vector with rank values (e.g. log2FC) and entrezids as names

Examples

myDE <- sqDE
rl <- seekGSErl(myDE, pFilter=0.05, colentrez="EntrezId")

Solatar/seeqR documentation built on Feb. 19, 2021, 8:07 p.m.