readSampleInfoFromGEO {limma} | R Documentation

## Read Sample Characteristics From GEO Series Matrix File

### Description

Read sample annotation from a GEO Series Matrix File into data.frames.

### Usage

    readSampleInfoFromGEO(file, remove.constant.columns = TRUE)

### Arguments

`file` | file name or path of GEO series matrix file.
`remove.constant.columns` | logical, if `TRUE` then columns that have the same entry for every sample are removed.

### Details

This function parses a GEO series matrix file. Sample characteristics associated with expression channels 1 and 2 are separated into separate data.frames. The function particularly allows for the fact that not every sample characteristic will have an entry for every sample.

### Value

A list with three components:

`SampleInfo` | character matrix of sample annotation.
`CharacteristicsCh1` | character matrix of sample characteristics associated with expression channel 1.
`CharacteristicsCh2` | character matrix of sample characteristics associated with expression channel 2.

Each sample corresponds to one row.

### Author(s)

Gordon Smyth

### See Also

An overview of LIMMA functions for reading data is given in 03.ReadingData.

### Examples

    # This example downloads a series matrix file of about 33MB
    ## Not run:
    url <- "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40115/matrix/GSE40115-GPL15931_series_matrix.txt.gz"
    download.file(url, "GSE40115.txt.gz")
    a <- readSampleInfoFromGEO("GSE40115.txt.gz")
    colnames(a$SampleInfo)
    colnames(a$CharacteristicsCh1)
    colnames(a$CharacteristicsCh2)

    ## End(Not run)

[Package limma version 3.50.3 Index]