geo_load_eset: geo_load_eset

In miracum/clearly-sigident.preproc: Sigident Preprocessing

geo_load_eset

Description

Helper function to load expression sets from GEO.

Usage

geo_load_eset(
  name,
  datadir,
  targetcolname,
  targetlevelname,
  controllevelname,
  targetcol,
  targetname,
  controlname,
  use_rawdata = FALSE,
  setid = 1
)

Arguments

name	A character string. The name of the GEO study.
datadir	A character string. The path to the directory to store the downloaded GEO datasets.
targetcolname	A character string. The name of the column in the GEO expression set's pheno data, holding the variable of interest (mapping information).
targetlevelname	A character string. The name of the the targets in 'targetcolname' (mapping information).
controllevelname	A character string. The name of the the controls in 'targetcolname' (mapping information).
targetcol	A character string. The columname of 'sample_metadata' holding the targets (default: "target"; caution: this should not be changed!).
targetname	A character string. Name of the the targets, specified in the 'target' column of 'sample_metadata' (default: "Target"; caution: this should not be changed!).
controlname	A character string. Name of the the controls, specified in the 'target' column of 'sample_metadata' (default: "Control"; caution: this should not be changed!).
use_rawdata	A logical. Indicates, if raw the data is downloaded in CEL file format, uncompressed and subsequently normalized with a GCRMA normalization, or if the already normalized datasets from GEO are downloaded (default: FALSE).
setid	A integer. Indicates, which set should be used by the software for subsequent analyses (default: 1).

miracum/clearly-sigident.preproc documentation built on June 28, 2022, 3:17 p.m.