In LiNk-NY/curatedTCGAManu: Presents example analyses using curatedTCGAData, MultiAssayExperiment, and TCGAutils

suppressPackageStartupMessages({
    library(curatedTCGAData)
    library(CNVRanger)
    library(ComplexHeatmap)
})

Load packages:

library(curatedTCGAData)
library(CNVRanger)
library(ComplexHeatmap)

Get the peaks:

peaks <- curatedTCGAData(diseaseCode = "*", assays = "GISTIC_Peaks", dry.run = FALSE)

Extract ranges + annotation alteration type (Deletion=1, Amplification=3)

grl <- GRangesList(lapply(experiments(peaks), rowRanges))

for(i in seq_along(grl))
{
    type <- substring(mcols(grl[[i]])$Unique.Name, 1, 1)
    mcols(grl[[i]])$state <- ifelse(type == "A", 3, 1)
}

Identify recurrent regions across cancer types:

pranges <- populationRanges(grl, density=0.15)
pranges <- pranges[order(mcols(pranges)[,2:1], decreasing=TRUE)]

Compute fraction of samples altered for each cancer type

getFrac <- function(gis, pranges)
{
    # compute diffs
    frac.altered <- rowMeans(assay(gis) > 0)

    # find overlaps
    olaps <- findOverlaps(rowRanges(gis), pranges)   

    # assign frac to pranges 
    # TODO: deal with duplicated subjects hits, 
    # ie several individual regions falling in a pancan region
    # options: largest region, highest diff, wmean 
    dd <- vector("numeric", length(pranges))
    dd[subjectHits(olaps)] <- frac.altered[queryHits(olaps)]

    # sign frac depending on alteration type 
    type <- substring(rowRanges(gis)$Unique.Name, 1, 1)
    sig <- ifelse(type == "A", 1, -1)
    dd[subjectHits(olaps)] <- dd[subjectHits(olaps)] * sig[queryHits(olaps)]

    return(dd)
}
frac.mat <- vapply(experiments(peaks), getFrac, numeric(length(pranges)), pranges=pranges)

Heatmap

colnames(frac.mat) <- substring(colnames(frac.mat), 1, 3)
hp <- list(title_position = "lefttop-rot",# legend_direction = "horizontal", 
            title="fraction amplified - \n fraction deleted")
Heatmap(frac.mat, heatmap_legend_param=hp,
        cluster_rows=FALSE, show_row_names=FALSE, row_split=pranges$type)

LiNk-NY/curatedTCGAManu documentation built on July 22, 2020, 4:06 p.m.