ivySE: ivySE: SummarizedExperiment for IvyGAP expression data and...

In ivygapSE: A SummarizedExperiment for Ivy-GAP data

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))

ivygapSE documentation built on Nov. 8, 2020, 8:08 p.m.