retrieveFromGEO {conclus} | R Documentation

## retrieveFromGEO

### Description

This function retrieves the count matrix and columns meta-data from GEO. They are formatted to be suitable inputs for conclus.

### Usage

    retrieveFromGEO(matrixURL, countMatrixPath, species,
    seriesMatrixName=NA, metaDataPath=NA, colMetaDataURL=NA,
    convertToSymbols=TRUE, annoType="ENSEMBL")

### Arguments

`matrixURL` | URL of the count matrix. The matrix must be un-normalized.
`countMatrixPath` | Path to the file to which the downloaded count matrix will be saved.
`species` | Values should be 'mouse' or 'human'. Other organisms can be added on demand.
`seriesMatrixName` | Name of the columns meta-data file hosted on GEO. This name can usually be found in the 'Series Matrix File(s)' section. Should not be used if colMetaDataURL is defined. Default=NA.
`metaDataPath` | If colMetaDataURL is used, defines the path to the file to which the downloaded meta-data will be saved.
`colMetaDataURL` | URL of the columns meta-data file hosted on GEO. This file can be found in 'supplementary file'. Should not be used if seriesMatrixName is defined. Default=NA.
`convertToSymbols` | Boolean indicating if the genes IDs contained in the row names of the matrix should be converted to official genes symbols. Default: TRUE. To choose the type of IDs contained in the count matrix, see the annoType parameter just below.
`annoType` | Type of the genes annotations contained in the row names of the count Matrix. Default: "ENSEMBL". See details.

### Details

The conversion (TRUE by default) of the row genes IDs (ENSEMBL by default) to official genes symbols is done with the function 'bitr' of the 'clusterProfiler' package. To see a list of all possible values to pass to the annoType parameter use 'keytypes' method on "org.Mm.eg.db" (for mouse) or "org.Hs.eg.db" (for human). For example, copy/paste in a R terminal: library(org.Mm.eg.db);keytypes(org.Mm.eg.db)

### Value

A list. The first element contains the count matrix and the second element contains the columns meta-data.

### Author(s)

Nicolas DESCOSTES & Ilyess RACHEDI

### Examples

    outputDirectory <- "./YourOutputDirectory"
    dir.create(outputDirectory, showWarnings=FALSE)
    species <- "mouse"

    countMatrixPath <- file.path(outputDirectory, "countmatrix.txt")
    matrixURL <- paste0("https://www.ncbi.nlm.nih.gov/geo/download/?acc=",
    "GSE96982&format=file&file=GSE96982%5FcountMatrix%2Etxt%2Egz")
    seriesMatrix <- "GSE96982-GPL19057_series_matrix.txt.gz"

    result <- retrieveFromGEO(matrixURL, countMatrixPath, species,
    seriesMatrixName=seriesMatrix)

    countMatrix <- result[[1]]
    columnsMetaData <- result[[2]]

[Package conclus version 1.0.0 Index]