preprocess_rawdata: Process raw data from GEO

In yin-huamin/Dbio: Bioinfo pipeline

Process raw data from GEO

Description

Process raw data from GEO

Usage

preprocess_rawdata(
  GEO_name = GEO_name,
  annotation = probe2gene,
  arrayType = Type,
  method.probe = "median",
  dir = dir
)

Arguments

GEO_name	GSE number
annotation	Probe anotation platform
arrayType	one of "AFFY", "AGI4-44K"
method.probe	one of "medain", "mean", "max", "min", default is "median"
dir	Des dir

Examples

library(Dbio)
# make file structure
initial_file("GSE54566", "./")
# get probe annotation data
annotation <- get_probe2symbol("GPL570", "GSE54566", "./")
preprocess_rawdata(
  GEO_name = "GSE54566",
  annotation = annotation,
  arrayType = "AFFY",
  method.probe = "median",
  dir = "./"
)

yin-huamin/Dbio documentation built on April 18, 2022, 4:41 p.m.