R: Diffuse large B-cell lymphoma

DLBCL {maxstat} | R Documentation

## Diffuse large B-cell lymphoma

### Description

A data frame with gene expression data from DLBCL (diffuse large B-cell lymphoma) patients.

### Usage

    data("DLBCL")

### Format

`DLCLid`

  DLBCL identifier

`GEG`

  Gene Expression Group

`time`

  survival time in month

`cens`

  censoring: 0 cencored, 1 dead

`IPI`

  International Prognostic Index

`MGE`

  Mean Gene Expression

### Source

Except of `MGE`, the data is published at http://llmpp.nih.gov/lymphoma/data.shtml. `MGE` is the mean of the gene expression.

### References

Ash A. Alizadeh et. al (2000), Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature, 403, 504–509

### Examples

    library("survival")

    set.seed(29)

    # compute the cutpoint and plot the empirical process

    mod <- maxstat.test(Surv(time, cens) ~ MGE, data=DLBCL, smethod="LogRank")

    print(mod)

    ## Not run:
      # postscript("statDLBCL.ps", horizontal=F, width=8, height=8)
      pdf("statDLBCL.pdf", width=8, height=8)

    ## End(Not run)
    par(mai=c(1.0196235, 1.0196235, 0.8196973, 0.4198450))
    plot(mod, cex.lab=1.6, cex.axis=1.6, xlab="Mean gene expression",lwd=2)
    ## Not run:
      dev.off()

    ## End(Not run)

    # significance of the cutpoint
    # limiting distribution

    maxstat.test(Surv(time, cens) ~ MGE, data=DLBCL,
                 smethod="LogRank", pmethod="Lau92", iscores=TRUE)

    # improved Bonferroni inequality, plot with significance bound

    maxstat.test(Surv(time, cens) ~ MGE, data=DLBCL,
                 smethod="LogRank", pmethod="Lau94", iscores=TRUE)

    mod <- maxstat.test(Surv(time, cens) ~ MGE, data=DLBCL, smethod="LogRank",
                        pmethod="Lau94", alpha=0.05)
    plot(mod, xlab="Mean gene expression")

    ## Not run:
    #  postscript(file="RNewsStat.ps",horizontal=F, width=8, height=8)
       pdf("RNewsStat.pdf", width=8, height=8)

    ## End(Not run)
    par(mai=c(1.0196235, 1.0196235, 0.8196973, 0.4198450))
    plot(mod, xlab="Mean gene expression", cex.lab=1.6, cex.axis=1.6)
    ## Not run:
      dev.off()

    ## End(Not run)

    # small sample solution Hothorn & Lausen

    maxstat.test(Surv(time, cens) ~ MGE, data=DLBCL,
                 smethod="LogRank", pmethod="HL")

    # normal approximation

    maxstat.test(Surv(time, cens) ~ MGE, data=DLBCL,
                 smethod="LogRank", pmethod="exactGauss", iscores=TRUE,
                 abseps=0.01)

    # conditional Monte-Carlo
    maxstat.test(Surv(time, cens) ~ MGE, data=DLBCL,
                 smethod="LogRank", pmethod="condMC", B = 9999)

    # survival analysis and plotting like in Alizadeh et al. (2000)

      splitGEG <- rep(1, nrow(DLBCL))
      DLBCL <- cbind(DLBCL, splitGEG)
      DLBCL$splitGEG[DLBCL$GEG == "Activated B-like"] <- 0

      plot(survfit(Surv(time, cens) ~ splitGEG, data=DLBCL),
           xlab="Survival time in month", ylab="Probability")

      text(90, 0.7, "GC B-like")
      text(60, 0.3, "Activated B-like")

      splitIPI <- rep(1, nrow(DLBCL))
      DLBCL <- cbind(DLBCL, splitIPI)
      DLBCL$splitIPI[DLBCL$IPI <= 2] <- 0

      plot(survfit(Surv(time, cens) ~ splitIPI, data=DLBCL),
           xlab="Survival time in month", ylab="Probability")

      text(90, 0.7, "Low clinical risk")
      text(60, 0.25, "High clinical risk")

      # survival analysis using the cutpoint

      splitMGE <- rep(1, nrow(DLBCL))
      DLBCL <- cbind(DLBCL, splitMGE)
      DLBCL$splitMGE[DLBCL$MGE <= mod$estimate] <- 0

      ## Not run:
       # postscript("survDLBCL.ps",horizontal=F, width=8, height=8)
        pdf("survDLBCL.pdf", width=8, height=8)

    ## End(Not run)
      par(mai=c(1.0196235, 1.0196235, 0.8196973, 0.4198450))

      plot(survfit(Surv(time, cens) ~ splitMGE, data=DLBCL),
           xlab = "Survival time in month",
           ylab="Probability", cex.lab=1.6, cex.axis=1.6, lwd=2)

      text(90, 0.9, expression("Mean gene expression" > 0.186), cex=1.6)
      text(90, 0.45, expression("Mean gene expression" <= 0.186 ), cex=1.6)

      ## Not run:
        dev.off()

    ## End(Not run)

[Package maxstat version 0.7-25 Index]