Package 'ivygapSE'

render design overview

Description

render design overview

render anatomic nomenclature

Usage

designOverview()

nomenclat()

Value

a rastergrob grob

Examples

designOverview()

---

simple plot of expression values by structure/expression-based selection in IvyGAP

Description

simple plot of expression values by structure/expression-based selection in IvyGAP

Usage

exprByType(sym, ...)

Arguments

sym	a gene symbol found among 'rownames(ivySE)'
...	passed to plot, exclusive of ylab, xlab, axes

Value

invisibly returns a list with two elements: exprs, the vector of expression values, and types, the vector of structure types

Examples

exprByType("MYC")

---

provide access to a limma analysis of RNA-seq profiles for reference histology samples

Description

provide access to a limma analysis of RNA-seq profiles for reference histology samples

Usage

getRefLimma()

Value

an instance of MArrayLM-class representing regularized gene-wise ANOVAs

Note

Uses download.file to acquire RDS of the output of eBayes from a public S3 bucket. The limma model was fit using duplicateCorrelation to address multiplicity of contributions per donor. Comparisons are to samples labeled CT-reference (cellular tumor, reference contributions), with coefficients 2-5 corresponding to CT-mvp (microvascular proliferation), CT-pan (pseudopalisading cells around necrosis), IT (infiltrating tumor), and LE (leading edge), respectively.

Examples

requireNamespace("limma")
ebout = getRefLimma() # is result of eBayes
colnames(ebout$coef)
limma::topTable(ebout,2)

---

simple app to explore image property quantifications in relation to survival and expression

Description

simple app to explore image property quantifications in relation to survival and expression

Usage

ivyGlimpse()

Value

Side effect of starting the app only.

Examples

if (interactive()) print(ivyGlimpse())

---

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))

---

demonstration of gene set construction for ivyGlimpse app

Description

demonstration of gene set construction for ivyGlimpse app

Usage

makeGeneSets()

Value

list of gene sets with attributes facilitating dropdown construction – attr(,"fullTitle") is a list of strings associated with gene set elements (named list with vectors of gene symbols constituting sets of interest)
List of 4
$ General: Ras-Raf-MEK-Erk/JNK signaling (26 genes)
: chr [1:26] "KRAS" "HRAS" "BRAF" "RAF1" ...
$ Glioblastoma: RTK/Ras/PI3K/AKT Signaling (17 genes)
: chr [1:17] "EGFR" "ERBB2" "PDGFRA" "MET" ...
$ General: PI3K-AKT-mTOR signaling (17 genes)
: chr [1:17] "PIK3CA" "PIK3R1" "PIK3R2" "PTEN" ...
$ Ovarian Cancer: Putative tumor-suppressor genes in epithelial ovarian cancer (16 genes)
: chr [1:16] "DIRAS3" "RASSF1" "DLEC1" "SPARC" ...
- attr(*, "fullTitle")=List of 4
..$ glioRTK : chr "Glioblastoma: RTK/Ras/PI3K/AKT Signaling (17 genes)"
..$ pi3k : chr "General: PI3K-AKT-mTOR signaling (17 genes)"
..$ ovtumsupp: chr "Ovarian Cancer: Putative tumor-suppressor genes in epithelial ovarian cancer (16 genes)"
..$ rasraf : chr "General: Ras-Raf-MEK-Erk/JNK signaling (26 genes)"

Note

Should be replaced by selections from a general catalog.

Examples

str(makeGeneSets())

---

helper functions for data access

Description

helper functions for data access

Usage

tumorDetails(se)

subBlockDetails(se)

vocab()

Arguments

se	SummarizedExperiment instance, intended to work for ivySE in this package

Value

data.frames for tumorDetails, subBlockDetails and vocab

Examples

data(ivySE)
dim(tumorDetails(ivySE))

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