dxsmall: dxsmall

In VanAndelInstitute/bifurcatoR: Hunt for bumps in high-dimensional (or low-dimensional!) data

dxsmall

Description

A SummarizedExperiment with covariates and mRNA counts from 501 AML cases.

Usage

data(dxsmall)

Format

A SummarizedExperiment object

Source

This data was created using inst/extdata/mRNA/dxsmall.reassemble.R

Examples

 data(dxsmall)
 show(dxsmall)

 # if `iSEE` is installed:
 if (require("iSEE")) {
   rownames(dxsmall)
   names(colData(dxsmall))
   table(dxsmall$FusionGroup)
   table(dxsmall$AgeGroup)
   iSEEapp(dxsmall)
 }

 # if `mclust` is installed:
 if (require("mclust")) {

   fit1 <- Mclust(logcounts(dxsmall)["MECOM", dxsmall$FusionGroup == "MLL"])
   plot(fit1, what="density", xlab="log(MECOM read counts + 1) in KMT2Ar")

   fit2 <- Mclust(t(logcounts(dxsmall)[ c("MECOM", "PRDM16"), ]), G=1:3)
   plot(fit2, what="classification")
   plot(fit2, what="uncertainty")

 }

VanAndelInstitute/bifurcatoR documentation built on Oct. 13, 2024, 6:29 p.m.