ivySE {ivygapSE} | R Documentation

## ivySE: SummarizedExperiment for IvyGAP expression data and metadata

### Description

ivySE: SummarizedExperiment for IvyGAP expression data and metadata

### Usage

    ivySE

### Format

SummarizedExperiment instance

### Details

Archive: gene_expression_matrix_2014-11-25.zip
Length Date Time Name
——— ———- —– —-
50585 03-31-2015 13:27 columns-samples.csv
86153820 10-31-2014 14:04 fpkm_table.csv
2015 11-24-2014 18:06 README.txt
1689619 10-31-2014 13:55 rows-genes.csv
——— ——-
87896039 4 files

### Note

Expression data retrieved from http://glioblastoma.alleninstitute.org/api/v2/well_known_file_download/305873915

### Source

processed from glioblastoma.alleninstitute.org; see Note.

### Examples

    ## Not run:    # how it was made
    ivyFpkm = read.csv("fpkm_table.csv", stringsAsFactors=FALSE,
          check.names=FALSE)
    g = read.csv("rows-genes.csv", stringsAsFactors=FALSE)
    library(SummarizedExperiment)
    imat = data.matrix(ivyFpkm[,-1])
    ivySE = SummarizedExperiment(SimpleList(fpkm=imat))
    rowData(ivySE) = g
    rownames(ivySE) = g$gene_symbol
    col = read.csv("columns-samples.csv", stringsAsFactors=FALSE)
    rownames(col) = col$rna_well_id
    stopifnot(all.equal(as.character(col$rna_well_id),
         as.character(colnames(imat))))
    colData(ivySE) = DataFrame(col)
    colnames(ivySE) = colnames(imat)
    metadata(ivySE) = list(README=readLines("README.txt"))
    metadata(ivySE)$URL = "http://glioblastoma.alleninstitute.org/static/download.html"
    # metadata(ivySE)$builder = readLines("build.R")
    de = read.csv("tumor_details.csv", stringsAsFactors=FALSE)
    metadata(ivySE)$tumorDetails = de
    subbl = read.csv("sub_block_details.csv", stringsAsFactors=FALSE)
    metadata(ivySE)$subBlockDetails = subbl
    bamtab = read.csv("bam.csv", stringsAsFactors=FALSE)
    rownames(bamtab) = as.character(bamtab$rna_well)
    bamtab[colnames(ivySE),] -> bamtreo
    all.equal(rownames(bamtreo), colnames(ivySE))
    colData(ivySE) = cbind(colData(ivySE), bamtreo)

    ## End(Not run)
    data(ivySE)
    names(metadata(ivySE))

[Package ivygapSE version 1.12.0 Index]