deal_geo: Pipeline of processing GEO data

In yin-huamin/Dbio: Bioinfo pipeline

Pipeline of processing GEO data

Description

Pipeline of processing GEO data

Usage

deal_geo(
  GEO_name = GEO_name,
  GPL_number = GPL_number,
  dir = dir,
  quiet = TRUE,
  rawdata = FALSE,
  Type = "AFFY",
  multiprobe = "median",
  removeRawdata = TRUE
)

Arguments

GEO_name	GSE number
GPL_number	Probe annotation platform
dir	Des dir
quiet	logical vector, default is FALSE
rawdata	logical vector, default is FALSE
Type	Type one of "AFFY", "AGI4-44K" when rawdata=TRUE
multiprobe	multiprobe one of "median", "mean", "max", "min", default is median
removeRawdata	logical vector, default is TRUE

Examples

library(Dbio)
# Download matrixs and preprocess
deal_geo("GSE54566", "GPL570", "./")
# Download, preprocess matrixs and keep rawdata
deal_geo("GSE54566", "GPL570", "./", removeRawdata = FALSE)
# Download, preprocess rawdata of affymetrixs
deal_geo("GSE54566", "GPL570", "./", rawdata = TRUE, Type = "AFFY")

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