preprocess_matrixs: Process matrixs from GEO

In yin-huamin/Dbio: Bioinfo pipeline

Process matrixs from GEO

Description

Process matrixs from GEO

Usage

preprocess_matrixs(
  dataset = expmat,
  metadata = sample_post,
  annotation = probe2gene,
  method.probe = "median"
)

Arguments

dataset	Expression matrixs
metadata	sample metadata
annotation	probe annotaion file
method.probe	one of "medain","mean","max","min", default is "median"

Value

preprocessed expression matrixs

Examples

library(Dbio)
# make file structure
initial_file("GSE54566", "./")
# get sample data
sample <- get_sample("GSE54566", "./")
# process sample
sample_post <- preprocess_sample(sample)
# get expression data
expmat <- get_matrixs("GSE54566", "./")
# get probe annotation data
annotation <- get_probe2symbol("GPL570", "GSE54566", "./")
preprocess_matrixs(
  dataset = expmat,
  metadata = sample_post,
  annotation = annotation
)

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