setRead: Get identifiers from a differential expression table

In Solatar/setR:

Description

Imports: dplyr, rlang

Usage

setRead(
  direction,
  path,
  path2 = "",
  sep = "\t",
  col_ID = Symbol,
  col_log2FC = log2FC,
  col_padj = padj,
  cutP = 0.05,
  cutFC = log2(1.5)
)

Arguments

direction	string, either "up" or "dn" (down), indicating that only rows with a positive or negative log2FC should be kept
path	string, full path to the file, including the file name
col_ID	string, the name of the column that should be used as an identifier
col_log2FC	string, the name of the column that should be used as the log2FC column
col_padj	string, the name of the column that should be used as the adjusted-p-value/FDR/qvalue column
cutP	number, p value cutoff. Rows with a number in col_padj higher than this number will be filtered out
cutFC	number, log2FC cutoff. Rows with a number in col_log2FC lower than this number wil be filtered out
set	string, indicating the separator used in the file

Value

a vector of strings (IDs)

Examples

IDs <- setRead("up", path=myPath)

Solatar/setR documentation built on Dec. 5, 2020, 10:50 p.m.